If your pH after injecting co2 is 5.5, the degassed pH is probably around 6.5 - 6.7, not too bad. It would be normal for tap water that has near 0 KH (like mine), if you are not adding anything to boost KH or anything that would be leaching KH into the tank to cause it to rise. Another issue that could crop up in low KH tanks is that if you're not removing enough of the waste from the substrate, or doing lots of water changes, whatever builds up causes the water to go acidic over time (say within a month of no water changes, or less depending on fish load). I know this doesn't answer your question, but the main reason for your low pH may have little to do with the GH booster.

As far as whether low pH is bad or not.... the general consensus seems to be that it's ok. My co2 tank has a pH probably down in the high 5's or at least low 6's and everyone seems happy, fish and plants.