I would agree with Rudi. Moving through Egypt is not far off from spending time in a Third World country.

I spent a good amount of time at the Cairo airport this year and it's a pretty unorganized, hectic place. We arrived from Beirut on EgyptAir and were attempting to connect to our OS (Austrian Air) flight to VIE. We were scattered helter-skelter by people that couldn't understand us and we couldn't understand them -- lots of "charades". Most of the time, we couldn't figure out if they were trying to arrest us or trying to help us out! In the end, they were trying to help us. Actually one security guard personally escorted us to our plane -- although he confiscated our passports and made us wait in a room for 45 minutes without explanation. We saw parts of the Cairo airport that, I'm certain, most tourists never avail themselves of.

What Rudi said about changing airports wasn't a joke either. The terminal where EgyptAir usually lands is almost a completely separate airport from the International terminal. We were "lucky" enough to have a personal police "shuttle" in the case mentioned above. Another time, we arrived at the airport and the cabbie dropped us at the wrong terminal... at 5AM. Needless to say, there weren't too many people around to redirect us! Luckily, a little "bakschis" (tip) will get you far in Egypt. I'm sure there's official transportation somewhere for transfers, but it sure beat me!

So, the answer to your question is: you may need more time! If you're unable to change your flights at this time, I wouldn't be super worried, but I would have a contingency plan in place.