Re: Help
Basically you need to respring into Safe Mode, and then respring normally as described in
this post.
If that doesn't work, read this, from
jailbreakQA:
Why is Cydia suddenly tiny after rebooting (the quarter screen bug)? How do I fix it?
Here are examples of what this looks like: on iPad, on iPhone. This is caused by having a tweak incompatible with iOS 6 installed, and it only shows up after rebooting. Check your tweaks and uninstall any that might not be compatible - this list may help. To uninstall incompatible tweaks: first put your device into Safe Mode using SBSettings (tap the "Power" button in SBSettings for the Safe Mode option) or using a similar tweak, or if you don't have something like that installed, you can reboot your device while holding the volume up button to disable all tweaks. Then open up Cydia and uninstall any tweaks that you suspect are incompatible. You can reboot again to check, and repeat the process as necessary.
Known tweaks that cause this issue are the current versions of Deck and Binary Clock, and old versions of SubtleLock, Incarcerapp, NowListening, Transparency, and RetinaPad (please update them if you have them installed). Respringing is a temporary fix for this issue (it will make Cydia usable again), but unless you remove the incompatible tweak(s), you will get this problem again the next time you reboot your device. Winterboard and UIKit Tools do not cause this problem (they are fully compatible with iOS 6), but installing/updating them may cause you to reboot your device, which makes the incompatible tweak problem show up.
(Source)