I had the exact same problem. I did the manual reset, tried to unplug it - everything I could think of. Nothing worked. I searched on the DTV site and found a solution.
Log into your DTV account - Under the Quick Links there is "My Equipment" and Activate Receiver, click that.
Near the top pf that page you will see a link to "Refresh your Service" Click that.
You will then be presented a list of your boxes, (Genie and mini genie clients). If you re-authorize the Genie itself that is what corrected the delay and pausing issues from the remotes for me. I had the same remote delays etc.. problem on the mini genies too.
Be warned, it will take about 24 hrs for the guide to catch up and put the TV series you record back into the To Do list but it does come back. Try and do this on a day before you record a small number of shows or no shows. You can manually add them into the To Do list but if you have a lot of them it is a pain.
It worked great for me. I was a little leery of the term 're-authorize' but it didn't effect my service at all - it just made my Genie start working like it did when I first got it.