I am trying to clean my mod and six times I have flagged three cells to be ignored and only one of the cells actually was ignored, in the File Details. The one cell that actually did get removed only did it on the fourth attempt. Two cells just will not be removed in order to clean the mod.

Is anyone else having this issue? I am up to date with patches etc...

Close the editor. 'I' marked records aren't actually removed until the CK closes, much like property subrecord data wiping, so your changes won't appear to have been made until reloading.