The V2 device runs multiple tasks at the same time. One of the tasks is to initialize and configure the SD Card for use. If the V2 can't initialize the SD Card, it just keeps retrying over and over until it can. The retrying uses CPU time that is then not available for other tasks - such as responding to key presses, which is why they were appearing to take so long. The only solution to a situation where FlashScan can't initialize the SD Card is to do what you did and reformat the SD Card in some other device.
Regards
Paul