When shifting rows using HSSFSheet.shiftRows(), the merged regions from the source area are copied to the target one, but the existing regions from the target area aren't removed. Would probably make sense to clear them, if we're copying the regions from the source area.
Is this still an issue? If yes, can you provide a short unit-test which reproduces the problem?
No update for a long time => closing this for now. Please reopen with more information if this is still a problem for you.