Thanks to the R5 forum:
The mail Rule documents are compiled and then each Rule is stored in "$FilterFormula", "$FilterFormula_0" etc. fields on the CALENDAR PROFILE in the mail file (use NotesPeek to look at this). Thus you have Rules documents AND Rule profile fields in a mail file.
Thus if you delete a Rule document in the mail file, before disabling it, the calendar profile still has the field that stores the compiled version of that Rule, so it still runs 8-o
If you have a Rule that you deleted the document for, before disabling the Rule, you need to delete the "$FilterFormula" fields from the calendar profile (or the entire profile) to solve the problem. But! If there are other Rule documents in the mail file that you want to keep, they will no longer function - You need to disable them and then enable them again (to that they are compiled & stored into the calendar profile again.
Storing compiled mail filtering Rules in the Calendar Profile?!? Now I have a sweet tooth, but that is too much fudge for my liking.