I haven't had that happen to me -- in that case, I'd suggest trying the following:
1. Take the flush valve seal off and then re-install it to make sure it's properly placed, or
2. Inspect the tower assembly to make sure it's not broken or otherwise damaged so it won't seal to the new flush valve seal. Replace that if necessary.
If neither of those procedures work, then it's probably time to call in a professional, because the problem may not be a simple matter of replacing the rubber flush valve seal.