1. Configuration file
Sent (3 different ones)
 2. Type of device and Firmware versions of al components involved, i.e. Pronto's, extenders, routers etc.
rfx9600's, tsu9400's, tsu9300. Hawking 300N's, latest firmware in B+G Mode. Fixed IP Addresses. Both on extenders and the rest of the equipment.
 3. How long does the IR continuation approximately last?
5-10 seconds.
 4. Occurrence of the issue
after wake up, often looses connection after a few "Command Failed"'s and then needs to reconnect (another ~5 Seconds). Set the timeout to 24 hours, but didn't do any good.
 5. Relevant messages in diagnostics log, i.e. those related to the issue
Extender didn't reply
 6. Is there ProntoScript involved? i.e. does the issue occur when a PS module is active or is there possibly PS running in the background. Or is the action initiated by a PS?
No prontoscript.
 7. Does the issue always occur with hard buttons or also with soft buttons?
Both

Posted it here for reference.
 
Edit: When I use WEP as Security Protocol I always get a 'Command failed' (Extender didn't reply). On WPA it works, but not well enough (the above issue). Seems to be most stable on WPA2, still not acceptable but slightly better than WPA.

Hoping for a quick solution, client's getting pissed as he "Hasn't been able to use" his system. (Ofcourse it's annoying if you simply want to change the channel or the volume and you have to wait 5~15 seconds to do so).