The first thing to get you to check is that your software and device firmware are all up to date.
Here are a couple of knowledgebase articles:
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Software
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Firmware
Depending on what version you are running presently it might be worth:
1) Copying all the tune and log files from the Data Filesystem using EFILive Explorer (ultimately a backup)
2) Resetting the FlashScan V2; press and hold the F1 key on the V2 keypad while supplying USB power
3) Format the Config and Data Filesystems
4) Reconfigure the Device and BBX functions as you desire
5) Program the device so that all the configuration and required scripts are copied down to the device
Hope that helps.
Cheers,