I have a weird set up, but I love it.... 8,10,13, 15, 18.. But I've never had any issues with the tuning... Just be patient. It may feel uncomfortable because it's so close in interval to your 12 or 14 (which ever you're using) so you're not going to get a perfect 3rd or 4th (as some drummers like to achieve) between them without some sound sacrifice. Try tuning the drum to itself, get the perfect tone for that drum, know what I mean??
I have a 13" tom as a first tom on one of my kits. what I do: Use a Pinstripe on top, and a snare side head on the bottom. the thing sings like crazy with the batter head tuned low, and the bottom head kinda cracked up.
Yeah, my only rack tom is a 13". Never have any problems out of it. I always use regular 2 ply coated (Emperor, G2, Response 2) on the batter and clear single ply on the bottom. I could see having a problem with a 12" and 13" rack tom setup, just trying to get a noticeable seperation between the 2 toms. My kit is 13", 16", and 18", so that's not much of a problem.
i used 2 hav a 13" on my practice kit, but then i went and switched it up a bit, so tht now all of my toms are 2 inches apart in diameter(and also depth, as a matter of fact), so tuning's not a problem now, nor was it back then as much either, and they sound so even and precise, especially when doin complicated fills
I don't mind using a 13" as a single rack tom, but I like to have a wide range when I use 3 toms (10",12",14"). A 12" and 13" seem too close in tonal range. If you want to tune them to a fourth interval, you can choke the 12 and have the 13 a bit below its natural range. The 2" difference seems to make it easier to find the intervals I want without under or over tensioning.