Yeah. If the bridge was not perfectly flat that definitely points towards it not being set up correctly. Guitars with a floating bridge are especially sensitive to it. Well, they're especially sensitive to pretty much everything. Even on my (non floating bridge) Strat, if I go from 10s to 11s, I have to re-intonate.
Actually it kind of reminds me of back when I was pretty new to guitar (a rich one, but still a noob), I tuned my JEM down to Eb, and it totally threw everything off.