Yeah it doesn't really fix the problem obviously, but since none of the mods I merged need any LODs that at least allowed me to use the program. I used v2.2.3.0 of Merge Plugins, updated to v2.3.1.0 (latest) to check and it behaves the same in that regard. After that I fiddled a bit with it and it turns out I had the "New Records" merging method selected, probably due to a misunderstanding on my part when I first configured the thing. Switching to the "Override" method generates a map file that is just like you described:
Wa Ribbon.esp=0
AirHelm.esp=1
00000D62=0005C00D
Sotteta Necromancer Outfit.esp=0
LinkleOutfit.esp=10
000012D6=0005C00E
000012D5=0005C00F
000012D4=0005C010
000012D3=0005C011
000012D2=0005C012
000012D1=0005C013
000012D0=0005C014
000012CF=0005C015
000012CE=0005C016
000012CD=0005C017
[...]About the old file, the rest of it is very much like the snippet I sent you, but here it is if you want to see it: https://pastebin.com/raw/B3ME5Q3U Since it seems to be a bug in the Merge Plugins program, if I may suggest, perhaps checking if the plugin name contains the string ".esp" and showing an error if not warning people to switch modes would be enough? The "Override" merge method seems to give me the same result so all that's really needed is telling people where the problem is IMHO. Thanks for the program btw, now I can see my house from afar