Well, got me that issue before with the IMG Guard IFF, also encountered that 'Bug' with the Kusari NAval Forces Guard IFF.
But I found a solution which is at least working, but pleaswe dont ask me why...
After your Guard reputations is full green (9 bars), buy your Guard ID and dock at any station you like, disconnect from the server and reconnect (not just change your character, disconnect and completly reconnect).
Use /droprep and disconnect-reconnect after everytime you used it.
When your Guard IFF is flashing, disconnect-reconnect, undock and dock, take a mission for the faction you have the Guard IFF for and fill up their representive 'normal' faction back to full.
Have you all done right, your IFF should be steady.
As said, dont know why this is working, but for the characters I had issues with the Guard IFF's with, this was the solution.
Thought it may have something to do with the rep-ninja, but no one else has had a problem.
Been checked by both Cannon and myself, and there is nothing obviously amiss.
I have set it manually now, see how that goes.
Hood
Some say he is a proud member of: "The most paranoid group of people in the Community."