I have some experience with compressor stall on aircraft APU's and ECS's.
First thing you need to do is familiarize yourself with the compressor stall charateristics. Your manufacturer should be able to provide this data. I am used to a plot the has corrected air flow as the x-axis (W * Sqrt (T[degR]/P[psia]) and the Press Ratio as the y-axis. The stall line is then plotted from lower left to upper right passing through lines of constant shaft speed in percent.
My APU stall experience has been due to hot gas ingestion which results in corrected air flow for relatively low press ratios. Make sure this is not your problem...
My ECS experience results from a very low compressor flow at high corrected speed. I would ensure that your air flow is what you expect.
The last thing I can recommend is to make sure you are using the right compressor for the job. Look at the compressir stall characteristics, and make sure you have plenty of margin. If you don't, think about another compressor.
Let us know how it goes. If you have more questions, just ask.