Not sure why, but all mycellium growth bonuses stopped working sometime after buying the auto-upgrader in gold... I have x7.37e6 growth bonus JUST from the first fire upgrade, but I am getting 41.92 growth/sec.
edit: Seems to start working after doing a gold reset... not sure what happened.
Edit 2: Seems to have an issue when buying the fire upgrade for 14 mycellium levels, and then it becomes much worse when you buy the 16 level cost upgrade. Does not seem to fix itself until you do a gold reset after that.
Final Edit for now: If you can get enough size to buy another Mycellium level it also begins working again. With no bonuses that can be pretty tough though.