Other posters have had different problems with alignment in the UI, this was caused by an unusual font size in the Windows 7 interface setup, might be worth trying a different size.
Don't see how font size would affect the audio waveform.
Some of the things that affect these programs aren't "apparently" logical. And clearly a lot of the things that become problems for the user base were NOT logical to become a problem to the design people.So ... it may not work for you, but as noted, for a number of people this actually did fix a problem like unto yours. Hope you simply checked it out on your rig.
I don't know how many times over the last couple years people have had a suggestion which ended up being the proper one but it didn't seem sensible to them so they refused to even try it and we had long threads where they were demanding a "sensible" cure ... and tried all sorts of other things ... and finally gave up and tried that utterly stupid suggestion that had been the first one and clearly had NO connection whatever with their problem ... and ... um ... amazingly, it worked.
Of course, some of them were nice but politely refused ... and some were a bit less than polite. Very frustrating as a volunteer to be attempting to help someone who isn't willing to try the suggestions nor even bothers to be neutral let alone polite.
I'm having this same problem on a mac and so is another editor. Doesn't happen all the time, but occasionally in CC zooming in and out will change the wave form, visually, but not the actual audio.
Real frustrating, because I'm editing 20 min shots looking for specific pieces of audio and I need to sync them as well. No solution, but you can try manually deleting the pkf file in explorer (should be next to your audio source) and then having premiere re-create the waveform.
...or try going to "Sequence" > "Render Audio". This might fix it as well.
Either way, this is something Adobe should be fixing first.