Problem: Headadd.cl distinguishes between star and skyflat images by assuming all starnames have an underscore"_" in them, and that all skyflats have have the letter string "fla" somewhere in them (and no underscores). It will probably get confused if this is not the case. It may also burp at you if your biases, or any other images, have an underscore or the letter string "fla" in them.
Solution: Use the IRAF task imrename to change the names of the offending files to suit this custom. I think it will work correctly if you simply re-run headadd (ie, "cl < headadd.cl"), but be extra careful to check the dates, times, exptimes, etc using hselect. If there is any uncertainty, check with ACL.