I was having similar problems like what you described.
I've found that using the .obj exporter from the older Blender versions (2.49b in my case) seems to cause the issue. I tried using the latest Blender to export the .obj file, which seems to have resolved the issue.
Just a heads up, the newer .obj exporter might output your model at half it's normal size. Fortunately you can adjust the scale of the output file in the export options.
I literally just discovered that solution about an hour ago, so might not be foolproof.