Same issue and then some here. The super building option doesn't work until I use the super unit option at least once. The building gets the 9999999999 for a second then returns to its normal max health unless, as I said, I first use the super unit option. Not a big deal really, except that in campaign mode it does, indeed boost the crap out of the enemy units as well.
I remember seeing somewhere that the trainer was meant only for skirmish though, not campaign. Oh well.
The first 6 options of the trainer are meant only for skirmish
the rest (option 7 to 0) can be used on campaign too
btw
I can confirm it too (game patched at 2.2) the Super unit function multiplies the HP of the enemies so you end up fighting enemies with 30000 or more wound