Legacy mesh format doesn't carry over UVs properly

Hello all,
At work I need to convert my 2.6x files to legacy mesh format in order to use them with a 2.49-only export tool (FLT) but I seem to have come across some sort of bug. I’ve been able to convert files which started in 2.49 back and forth with no issue, but if I export a file created in 2.6, the texture links associated with the UVs are broken. The appropriate textures are still linked to the file, and the UVs themselves are all right, but the objects appear white because no textures have been assigned to them. (That is, TexFace textures applied without materials.) If I assign the textures in 2.49, the models will continue to carry them no matter which version of Blender I open them in, and changes made in 2.6 will be carried over properly. Any idea what might be causing this, and if there’s a viable workaround that would save me having to re-link all the textures by hand?