Import/Export OBJ problems

I’m trying to use blender to make some modifications to a pre-existing model, which uses an obscure file format (mdl). However, it seems fairly similar to the obj file format, so I just wrote a simple script to convert from mdl to obj and back again. The file seems to import fine, but when I export it as an obj, slight distortions are introduced into the model (i.e. vertices off by a millionth of a BU) even when I don’t make any modifications. I know that little of a difference sounds insignificant, but the model I’m editing is part of a larger model, and these slight deviations prevent it from being “water-tight”, which is essential to what I’m doing. I think the problem is related to the import, because I see these same distortions when I try exporting it with different file formats. Does anyone have any ideas?