Egypt’s protracted series of parliamentary balloting has just begun, but it is not too soon to think about the implications of presidential elections that have yet to be scheduled. And indeed, the way those elections have been planned (or, more accurately, the way they have not been planned) should cause deep concern.

On November 23, the Supreme Council of the Armed Forces (SCAF) made an apparently major concession in the face of large demonstrations in Tahrir Square and severe criticism from across the political spectrum. It pledged that presidential elections would be held by the end of June 2012, following which the SCAF would hand its tremendous constitutional power over to an elected leader.

But the terms of that concession were never spelled out and much depends not simply on whether it is honored but how it is honored.

To understand why Egypt’s badly-designed transition may soon encounter another crisis, it is necessary to examine the fine print of Egypt’s March 30 “constitutional declaration”—the country’s current governing document. When it issued the document, the SCAF, acting through its legal drafters, planted two time bombs. One involves the powers of the parliament and it is already exploding. The second involves the relationship between the SCAF, the presidency, and the constitutional drafting process.

The first time bomb was noticed by only a few observers at the time, but it seems to have been planted deliberately: the parliament Egyptians are electing now has a very ambiguous set of powers. It does have a circumscribed legislative role, but it must share that with a SCAF that can rule by decree, and it has no clear authority over the cabinet. Only in the last few weeks have Egypt’s civilian politicians, especially those in the Muslim Brotherhood, realized that they might find themselves in a weak constitutional position if they attempt to use their parliamentary position to write laws and oversee the executive.

But the second time bomb, involving the timing of presidential elections, has drawn virtually no notice—yet. And it seems to have been placed as much by accident as by design. The SCAF’s initial statements of a transition sequence began with parliamentary elections followed by presidential elections and the drafting of a new constitution. The package of constitutional amendments Egyptian voters approved in a March 2011 referendum provided for a new president to be elected. There would be no reason to include such a provision unless presidential elections were to precede the new constitution. And sure enough, the March 30 constitutional declaration incorporated those amendments just approved by voters. Indeed, it even promised that the SCAF would continue to exercise its enormous prerogatives only until the completion of presidential and parliamentary elections. After that point, it would presumably revert to its former position, simply at the apex of the military rather than the ruler of the nation.

The declaration thus implied a sequence: the parliament would be elected; the SCAF would summon parliament to elect members of a 100-person constitutional drafting body; presidential elections would be held as the document was being drafted; and the finished draft would be presented to the people in a referendum. But while such a sequence was implied, it was not required. And the SCAF was curiously silent about when presidential elections would be held.

But in reality, the silence was not so curious. Having issued this document, members of the SCAF seem to have realized that once presidential elections were held, the SCAF would lose its ability to make sure that their favorite provisions were inserted into the constitution. And those provisions, it gradually became clear, would exempt the military from any civilian oversight and give it an autonomous and powerful voice in security affairs.

The SCAF’s solution was audacious: it sought to postpone the presidential elections until after the constitution was adopted and also took strong steps to dictate the process by which the document would be written and what it would say. And it did so through sponsoring the development of a set of “supraconstitutional principles” that would dictate the composition of the body writing the constitution (an odd reading of the provision in the SCAF’s own constitutional declaration that the parliament elects that group), place the military beyond effective oversight, and give the SCAF a permanent supervisory role.

The SCAF had clearly reached too far—its effort sparked a strong reaction from a wide range of political forces. Even some liberals who had seen the SCAF as a bulwark against Islamists joined in the chorus of denunciations and the White House issued a vague but definite public rebuke.

And so the SCAF backed down by pledging to hold presidential elections by June 2012. But its apparent concession could quite easily contain the seeds of a new crisis and set off the second time bomb in the constitutional declaration.

What the SCAF failed to do was to pledge to carry out presidential elections before the constitution is written. And while it has not said anything more on the “supraconstitutional principles,” it has not repudiated them. There are limited indications that the SCAF intends not to change the sequence at all but simply to rush the process at breakneck speed—to have the constitution written immediately and then move to a referendum, all before the new president is elected. This kind of schedule would not only leave the SCAF in total control over the process; it would also be extraordinarily, even unrealistically, quick.

Two little noticed details make such a timetable a special concern. First the “supraconstitutional principles,” if they are dusted off, will give the SCAF still more power over constitution drafting if the assembly does not meet the deadline. Second, the entire process would take place under the shadow of a state of emergency that expires in June of 2012 (according to the person who led the drafting of March’s constitutional amendments, the state of emergency rubber stamped by the Mubarak-era parliament should have expired, but the SCAF advances—and enforces—a rival interpretation that leaves it in place until June).

Thus the SCAF’s concession may simply leave Egyptians with an unworkable, rushed process that leaves the military’s levers of control more powerful rather than less.

Parliamentarians now being elected may therefore find not only that they cannot oversee the executive or stop the SCAF from writing laws, but also that that their most significant task—naming those who will write the constitution—has been robbed of much of its force by the generals.

To describe these loopholes as time bombs waiting to explode may go slightly too far. What both the SCAF and Egypt’s largest political party, the Muslim Brotherhood’s Freedom and Justice Party, have shown to date is a willingness to play bare knuckled politics while avoiding full confrontation. It is unlikely that the SCAF’s haphazard drafting will lead to a total breakdown of the transition process. But it could lead to yet another crisis in a country that shows strong signs of weariness with its current protracted—and indefinite—state of political uncertainty.