I have the same issue, at first I thought I had solved it by downgrading back to firmware version 1.0 (which I had issues with as well), but it seems this did not solve the issue.
With Flirc v1.0.0-rc4 I had the following issues (at some point):
No more space for new buttons when programming a button.
Unable to erase buttons.
Unable to clear configuration with Flirc GUI (it says it is cleared, but it is not).
Unable to upgrade firmware to version 1.0. Flirc GUI application crashes.
Buttons wrongly mapped.
At first I tried installing Flirc v1.0.0-rc3 to see if I could downgrade with/to that version. That did not work.
After this I installed Flirc v0.96 and did the following:
Clear configuration with Flirc GUI, this worked.
Tried to downgrade firmware (using upgrade option in Flirc GUI) to version 1.0 with fw_1.0.bin, this failed with Transfer error and Flirc GUI crash.
Restarted Flirc GUI and tried again to downgrade to 1.0, this time the downgrade to firmware version 1.0 with fw_1.0.bin succeeded.
After this I was able to program buttons again using the Flirc v0.96 GUI.
After programming multiple buttons for my Logitech Harmony One however I noticed again the issue described in the first post. I think I first noticed it after a power down (to stand-by mode) of my Windows 7 PC. When it was powered on again some buttons did not work anymore and some had different response than how it was programmed/recorded. After this I had again trouble erasing buttons and recording/programming buttons.
Hope this can be solved in a future release soon because it indeed makes the Flirc more or less useless. :-(
Next to this I have some requests (I am new to this forum, so I hope it is OK to post them here):
Make text for firmware verion in Flirc GUI smaller. I have my mediacenter desktop resized to 150% and firmware version is unreadable.
If Button already exists add option to overwrite (next to Cancel and Redo).
Let me end by saying thanks for making Flirc available for us. It is a great product. Keep up the good work!!!