The ignore list is relatively new to EQ2Maps but has nothing to do with LU53. The colored dots are actually older than the current rev of EQ2Maps, you're icon files were probably getting overwritten by the patcher.
If you prefer the newer EQ2Maps icons, you can remove
Code:
<File Name="_Skinnable_POI_Icons.xml" />
from eq2map_ignorelist.xml
Be aware that this will set all POI icons to stock EQ2Maps and disable the couple additional POI types I added.
I personally found some of new EQ2Map icons less obvious/identifiable than the old fashion simple colored dots from the original EQ2Maps, so I changed them. IMO 100+ little black stick figures don't stand out so well.