A friend of mine has been having this same problem, and we can't fix it either. I can provide a bit more information on the subject, however.
I have a server and every time he tries to connect, this shows up on the console:
2014-03-16 17:51:05 [iNFO] [ForgeModLoader] User I'm removing his IGN connection fail
ed: missing [], bad versions [MineFactoryReloaded|CompatForgeMicroblock, MineFac
toryReloaded|CompatRailcraft, MineFactoryReloaded|CompatMystcraft, MineFactoryRe
loaded|CompatRP2, MineFactoryReloaded|CompatAtum, MineFactoryReloaded|CompatTher
malExpansion, MineFactoryReloaded|CompatXyCraft, MineFactoryReloaded|CompatAppli
edEnergistics, MineFactoryReloaded, MineFactoryReloaded|CompatBackTools, MineFac
toryReloaded|CompatProjRed, MineFactoryReloaded|CompatForestryPre, MineFactoryRe
loaded|CompatIC2, MineFactoryReloaded|CompatVanilla, MineFactoryReloaded|CompatT
haumcraft, MineFactoryReloaded|CompatPams, MineFactoryReloaded|CompatExtraBiomes
, MineFactoryReloaded|CompatChococraft, MineFactoryReloaded|CompatTwilightForest
, MineFactoryReloaded|CompatBuildCraft, MineFactoryReloaded|CompatForestry, Mine
FactoryReloaded|CompatSufficientBiomes]
If any seniors to AOTBT are familiar to this problem, tell me what you did to fix it.