Can comments in stored procedures cause problems
I've never heard of comments causing a problem.

The code you captured from the running server and the posted source are for different SPs.  It makes me think that maybe the ..SU01 version is still in your database and being executed (from a job perhaps?) whereas you are trying to debug the ..SU012_XML code.

For testing you could add another INSERT to the SP, writing as single value to a dummy table.  Then if the commented-out lines run there will be more rows in the dummy table than expected.