I've got a Strat style whammy bar bridge that came standard on my guitar, a J3 Phoenix. It hasn't had any problems at all until about two weeks ago when I tuned the guitar up a whole step from D to E standard, and it was only a little while after that that I noticed the bridge was being pulled by the tension of the strings into a bent position to the rest of the body, maybe being a half cm from it's normal position against the body. I was slightly confused by this considering I had had the guitar in every tuning from E standard to Drop-C before this and seen no effect on the bridge, and The strings I presently have on it are only a little stronger than my old ones, I think that I went from a 48-10 to a 52-11 gauge set.

I'm not sure if this is, but am worried that it will be a potentially damaging problem. If the solution is to either down-tune it once more, to get smaller strings, or to somehow adjust the springs in the bridge, I would like to do nothing unless I have to. Any suggestions?

Anytime you move up to a thicker gauge string you will have to adjust the strings on your tremolo "release the tension" to level off the bridge again.

Tighten the springs in the back of the guitar to pull the bridge back down

I'm having a similar problem as brosefstalin
I've been experimenting a lot recently with detuned tuning
I have a floating bridge (floyd rose copy)
as you downtune the guitar, you have to loosen the screws at the back to bring the bridge back up
but now I want to be in standard tuning,
I can't really tighten the screws at the back any further, and the bridge is up really high
and the tuning is still too low
so I'm not really sure what to do about this one

if anyone has any advice it would be greatly appreciated
thanks

Try loosening the stringgs and then re tuning.
Sometimes floyd rose trems need to settle after adjustment

I've got my guitar to a state where the tuning is all half a step down with the bridge being level, so that's an improvement definitely

I'll give it some more tweaking and loosen the strings,

Thanks