Elk not playing nice with ISY

I have an issue with my ISY's coordination with the ELK. If I try to run a program from my ISY, I have to sometimes wait up to 20 seconds before the ELK will respond.  I have been trying for months to trace down the problem with no success. 
 
When I presented this problem on the U-D forum, most people feel I have a program(s) that is looping, causing the delay. But it is not obvious from the ISY that a program is 'looping'.  I recently upgraded from the 99i to a 994i and have to admit there was little or no change.
 
Now I noticed the last few weeks, programs that should execute when my garage door opens (zone violated) are no longer doing so.  So my latest theory is the the link between the ISY and ELK is the problem.  Is it possible the M1EXP card is not performing as it should or failing in some way?  Is there a test that can be performed or a fix (like rebooting card)? 
 
Any help will be appreciated as I cannot find anyone else that has experienced this 'delay' issue.
 
This ia a difficult problem to figure out without some additional information. I would suggest the following steps:
 
1. Test the physical wire connections between Elk and Isy and M1EXP card and main board, you may have to eplace the serial wire.
2. If you have other M1EXP cards, swap one with the Elk and see if the problem transfers
3. Get ComDebug program, connect your PC to Elk and see what Elk sends when your garage door is opened, and if it is timely
4. If step 3 looks good, test the Isy port, is anything is sent to Elk when it should be?
 
Once you get answers to the above you may have a better chance at solving your problem.
 
Have you restarted your Elk?  (Power down and then Power up?)  I have had a similar problem with my PC using Elve.  Elk sends commands to Elve on a timely basis (using Elve for text to speech when a door is opened for example) however Elve is also sending commands back to the Elk (when a door is opened open a couple of relays to mute some speaks so the zone announcement can be heard).  The relays should trigger right before the TTS announcement starts.  This worked fine for quite a while but I started to notice a delay in the music muting which seemed to get worse the longer my Elk was running.  Eventually it got to the point where the relays were being switched by the Elk probably 10 seconds after Elve (I believe) was sending the command.
 
Restarting the Elk by powering down and back up seemed to have brought it back into sync so I can only assume that there is something in the Elk that eventually builds up and causes this delay.  I figure I will have to power down and back up every few months.
 
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