This answer is a little late.
I have encountered this issue a couple of times till now. It happened even for the same models, just with some slight changes to net widths, and this error occurs. If your settings are right, and your model has passed the validation check, then it could be a bug. You should send your model to Ansoft for them to rectify the bug in the next revision of TPA.
While i know it is irritating, i can offer you a couple of alternatives:
1) Use Q3D to extract the same nets
2) Use HFSS to obtain the S-parameters, then extract RLC from there.
3) Use ADS EMDS to obtain S-parameters, then extract RLC from there.
4) Use SI-wave to extract S-parameters, then extract RLC from there (u must have a solid ground plane here.)