The problem is essentially that I have a quest that is meant to start from another quest's stage fragment. The line is simply Second.Start(), and I've verified several times that Second is filled with the proper quest. However, my debug log gives me this:

[PCKP_Qst_JoinKeepers (03000830)].QF_PCKP_Qst_JoinKeepers_030012D9.Fragment_5() - "QF_PCKP_Qst_JoinKeepers_030012D9.psc" Line 77[01/03/2013 - 06:22:36PM] error: Cannot call start() on a None object, aborting function callstack:

No idea what's going on.
All the aliases in the second quest are optional, as not all of them are initially filled. Dunno what is happening here.

EDIT: I think I figured out what the problem is. While I can refill the property that was left blank by my TESVEdit merger, the property will NEVER work again. Any fragment property seems to behave this way, once it has been emptied by a Edit injection it doesn't want to work ingame, though you can refill it in CK. This may have to do with the fact that I have a master file, going to espify and see if that helps.

TES5Edit doesn't process VMAD subrecords that hold script properties. You should always fix them in CK after merging. At least with the current version of TES5Edit.
Tthe next one will support VMAD.

Problem was that I couldn't fix them afterwards, eventually I worked out that this was because I was using a master file. By espifying it and reworking the properties then, I managed to fix it.