Powering on VCC and VS seperately is allowed and is not any problem. The resistors for low current signals are uncritical, as long as the GND connection is stable. Most probably, you have a layout problem - please see here:
Do you use a two layer layout? Have you gone through the checklist?
If you want, you can post a link to your layout, or email to tmcinfo at trinamic dot com for comments from our side.