Hi Pete,
I have a couple thoughts that may be causing your issue. If you are using the SB3 wirelessly, it could be as simple a a congested network because of neighbors, or perhaps there is an issue with your network or router. You may want to try a different channel through your wireless router and see if that helps.
Another possibility, the CPU may be spiking for various reasons. Were you ripping music when you noticed the disconnects, or is your laptop running other programs in the background? Maybe even a driver issue. You may want to monitor your CPU usage (via windows or an external program) while playing, ripping, etc. and see if you can duplicate the timeout and see what the cpu monitor has to say.
I have been using my Transporter for a better part of a year, and have become fairly proficient with the software, plugins, setup, tagging, etc. I would be glad to help with any questions you may have. PM me if you would like, and we can talk on the phone.
Take care,
Mark