Im aware this may be a conflict with another plugin but I dont have a plugin (with the exception of quicksmelt) That would change small furnaces.. Does anybody else have this problem or a solution?

what is actually 'not working' - if you were more clear, and could give steps to replicate your problem. It would also not hurt to share your full list of plugins either.

i found the problem for anyone that has similar results as mine.

basically when updating to the latest version something went wrong and all of the preset stack sizes in furnaces were changed. if you have a setting too low / too high it wont allow inventory put into the furnace.