It's an awkward use of the idiom. Usually, "so much so that" refers to a positive measurement of something, not the negative lack of something(as in your example). The example provided by Google's online dictionary is:
I was fascinated by the company, so much so that I wrote a book about it.
Another example of my own uses the volume of a fluid:
He overfilled the car's gasoline tank, so much so that the floor is covered with gas.
The way I'd structure your phrase is:
I rarely log onto Skype, it's so bad that I only just now saw your message, though you sent it a week ago.
In this case I'm using the idiom "it's so bad that," which is a negative version of the positive "so much so that."