I had a similar problem but there is one significant difference:

In my misshap the amp was dead once it cut off and wouldn't work unless reset from the power switch - also the green led on the front slowly faded to off and stayed this way - this behaviour would indicate an overload detection.

Since yours is going off and then comes back on by itself, I would rather think that this is the thermal protection kicking in.

I'm afraid a call to M is in order.
Best of luck.

M kit : G08 502 557 507 2xDSP5k