I agree, one/some of the ML files on the card you used could be corrupted/missing, so refreshing the ML files is a good idea.
Alternatively, could the version of ML on the card you used be either not up-to-date or for a different model camera (again, refreshing the ML files would identify this)?
Also, just an FYI as I have a 600D (so using a different model camera), but I have not noticed any intervalometer issues after nearly 4 years of use of ML & this is mostly what I use ML for, don't use many other features at all (wish I had the time to learn them!).
Good luck with your trouble shooting and keep us informed of your findings.
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