Okay I know a lot of people have had this happen but I'll explain what occurs.
If more than one guild attacks a controller, there seems to be no clear cut victor. So, the 20 min timer clicks down and then one of the guilds can build but right after building (boom - you are now in 25% suppression). The reason why it happens is because former bases are 25% suppression for 2 hours.
Why does this happen? Its utterly stupid. Right after you build your controller, you then have to stand around for 2 hours fighting off the forces you just finished defeating with only a lone controller there. If you get overrun (which happens a lot), they attack your tower and you lose the spot you just gained. This has happened to me or someone else I know 3 out of 6 times now.
Take away the 25% crap on NEW towers and force them to 100% period. I don't mind former bases and control towers going to 25% for the penalty but don't put the new tower freshly built at 25% after taking a base.