Brand new frame: rear dropouts too small?
 

I have a brand new track frame with horizontal rear dropouts and a brand new wheelset that I'm trying to use.

Unfortunately, the rear axle is just slightly too large to fit into the dropouts. It looks like I could file off the paint inside the dropouts and make it fit...but I was wondering if this is something normal that is done with a new frame.

The other bikes I own have all the paint scraped off inside the dropouts.

Do you mean that the diameter of the rear axle is too large to fit in the dropouts?
Or, that the spacing of the locknuts on the rear wheel is too wide to fit between the rear dropouts without stretching. It sounds like the latter, but you certainly didn't write your post in such a way as to make sure we know what you're talking about.

Most track frames are spaced 120mm between the inner sides of the rear dropouts (and yes, I know that they're not technically dropouts on track bikes, but that's the standard term for the place where the rear wheel's axle slides into, so I use it in reference to track bikes too).
Some track frames designed for Japanese Keirin racing have 110mm rear spacing.
If the difference is just thickness of paint, you're not dealing with a 10mm difference. Here's what you can do:
* stretch the rear dropouts slightly apart when you're putting the wheel in. This is completely fine if it's still, and basically fine with aluminum if it's 1-2mm.
* remove a spacer or two from the hub's axle

Maybe his wheel's 10mm axle is too thick to smoothly slide through the trackends? If that's the case, perhaps there's too much paint there?? A little filing wouldn't hurt...

Yes, this is what I meant. I'm sorry if my post wasn't clear on this.

I've been doing some filing this morning and it almost fits now...

file the bottom part of the dropout, that way the wheel should sit straight even if you file unevenly.