Some problems on the SD card make the TT refusing it. See the Tom Tom site for details: These tools do not fix all problems.
Flash can be corrected (and formatted) using the normal disk maintenance tools of your OS (FAT32). The most important problem is that the FAT file-system is not suited for flash memory, especially large ones (You cannot use another file-system).
If your device is new enough, you may be eligible for Tom Tom's latest map guarantee that gives you one free map update within 30 days of the purchase of a new Tom Tom device.
Our XL 340 S Live was outside of the window of opportunity.
These navcores can be used on TT's that were not made to use them (e.g. SE navcores do not require additional patching (they are already very heavily modified). The bootloader is hardware specific, not navcore specific.