I have the keypads with a keyed deadbolt too, because I'm afraid of the pad malfunctioning or something.

The company that manages our properties (granted the company is owned by the same dingo that owns the turnkey company I work for) only charges for items when they are relevant (IE they don't mow grass in the winter, although they do shovel snow if the property is vacant)@Sriv Nava If a toilet flapper malfunctions within the first year of ownership, my investors wouldn't even see a charge from the PM company, let alone one that is $45/Hr for labor.

I used my handyman once to replace without a permit but then I got to thinking about if for some reason the tank malfunctions and causes injury, I'd be liable and insurance wouldn't pay so for the small cost compared to leaving yourself exposed, its worth having a plumber do it and pull a permit.

Because no device can be 100% reliable, you have to balance the benefit of the device in the market (people get healed) with the risk of device malfunction (worst case, people die).  

If the clog is due to malfunction I fix it.

But I can tell you that is perfectly safe 99% of the time unless there is a facility malfunction resulting in a catastrophic failure (blowing up).

I had the water company out to check the meter for a leak or malfunction and that proved to be fine too.I didn't want to believe that it could be one of my new tenants but with everything else crossed off my list I don't know what else to think although I don't know who it is.

They have the tools to run diagnostics and tell you exactly what is malfunctioning.

I attempted to do so and it keeps malfunctioning.  

It is possible there is a malfunction that short cycles the system, or, the tenant is just overly sensitive/demanding.