Ok, third time lucky; I opened the phone again and took a look at the battery connector under the microscope. I'm pretty sure I found the problem: the PolarCell battery actually has the wrong connector for the N9, or the plastic housing for the connector has been incorrectly moulded - it had a protrusion on the left-hand side which didn't quite fit in the connector on the N9, causing the connector to be pushed sideways to the right by about 0.3mm when inserted. This in turn caused the three thin terminals in the N9's connector to bend slightly, particularly the left-most one (positive). Furthermore, the plastic around the positive terminal on the battery's connector was poorly moulded as well, and a small piece of extraneous plastic was present which caused one half of the terminal to be held back inside the housing. This was on the right hand side when the connector was inserted, so the two effects may have worked together to cause a very unreliable connection (the left-most terminal pin got bent away from the good half of the positive terminal on the battery's connector). I took a scalpel blade to it under the scope and carefully trimmed the protrusion and freed the inoperative half of the positive terminal, reassembled and all seems good; no amount of shaking, or pushing/flexing the screen or case, causes the phone to reboot or shut down. Hopefully that's the last of it.