Since you decided to update, you lost cIOS249. You need to reinstall a lot of stuff now.I did some searching and eventually read up on this freeze being IOS issues. I downloaded cIOS installer to try and fix the problem, but when asked to chose an IOS to work with, I chose 249 and the console freezes on me, just like when reading the PAL game disk.
Check here for more info on affected homebrew after the 4.3 update.
New System Menu Update 4.3 - GBAtemp.net