Shouldn't be an issue. I use ProSeries but have people that come in with multiple IHSS W2s with the same situation, I just enter them as they appear and it all works fine.  Its not an uncommon situation, all the IHSS W2s have the same FEIN on them, and different state ID #s.

DIY programs like Turbotax may have an issue with it, but any professional tax software should handle ist fine.