The font height changes in DejaVu at that point size because font height information between the two normal and the bold font is different when it should be the same.
The DejaVu Sans Mono 10 font that I use doesn't change the font height between normal and bold weight. I set that in my .emacs with
(set-frame-font "DejaVu Sans Mono-10")
So you have something to compare against, the info for "DejaVu Sans 10" font via (font-info on Emacs 25):
(font-info "DejaVu Sans Mono-10")
["-unknown-DejaVu Sans Mono-normal-normal-normal-*-13-*-*-*-m-0-iso10646-1"
"DejaVu Sans Mono:pixelsize=13:foundry=unknown:weight=normal:slant=normal:
width=normal:spacing=100:scalable=true" 13 17 0 0 0 8 13 4 8 8
"/usr/share/fonts/truetype/dejavu/DejaVuSansMono.ttf" (opentype ((DFLT ...) )))]
EDIT based on subsequent info:
In the font information above, I show a font height of 17 and you report a height of 15 (normal) or 16 (bold). In emacs 25 there is additional font information after those 3 0's, in particular the font descent is 4.
Although I don't have a problem on Emacs 24 or 25 with DejaVu Sans Mono and the Bold variant, the simplest thing is to use a font and size that doesn't change width (as shown by font-info) between normal and bold or something other than DejaVu.
As for what's causing this, it might one of your libraries, (my gtk is libgtk-x11-2.0.so.0), but I doubt it would be this particular library. Also doubt it is the ttf file or package. More likely is the freetype rendering (I have libfreetype.so.6). Since DejaVu are scaled as are the other fonts that do work for you, a computation error tickled by the way DejaVu was written would explain why these work at some sizes but not others.
To verify whether the problem is Emacs specific or not, you might be able to bring up two terminal windows, one with a bold prompt and one without and compare the line spacing on them. If it's different like Emacs, then this has to do with the rendering and/or font.
If you compiled emacs there might be something going on there.