Oh, right. On using the flash tool, is XIM solid blue before using the tool? If so try using other ports on the PC, USB 2.0 ports if available.
About your key issue, it may just be an issue with the keyboard because there have been no hardware or config changes and the issue doesn't happen with another keyboard.
If the keyboard allows for reassigning buttons or macros maybe check if there is PC software for the keyboard that can factory reset it.
If you would like I can move this thread over to Hardware Compatibility where it will be seen by more people who may have the keyboard and be familiar with this.