Someone who knows more about NMR feel free to correct me if I'm wrong, but I believe a negative peak indicates a quaternary carbon.
No, a DEPT90 should only have CH peaks, and they should be positive (as Honclbrif says).
I think you're thinking of a DEPT135, which has CH and CH
3 positive, and CH
2 negative (quaternary are absent).
It sounds like a processing issue to me. I have come across it a couple of times in the past, and by fiddling about with the apodisation of the FID in MestreC I got a decent spectrum out of it. It was a very unsophisticated process, basically trial and error, so I can't give you instructions. At that time we got pdfs sent to us, which almost always looked fine, so the processing software attached to the machine was OK - it was my personal processing software that wasn't handling the raw data for some spectra very well.
Do you have dedicated NMR staff you can ask? Contact the manufacturer?