I'm not sure if there is an input jack issue as such or if there just a problem with making sure that the jack is fully inserted.
I had this happen to me once, early on, with a cheap lead. Clocked the odd levels during the support so checked everything over in the gents and found the minijack lead not quite fully inserted. No problems since, even with that same lead.
I think if you take care to plug in properly, this problem should effectively resolve itself. After all, it's a 3.5mm connection, it's hardly secure under the best circumstances and I wonder if the slightly stiffer action that seems to be causing these problems might actually work in its favour if the lead is subjected to the occasional tug during use.