How far away and how many walls between the Hubitat Hub and the Garage Door Controller?
This sounds like a Z-Wave range issue and not a frozen Z-Wave. Move the hub closer to the controller and test.
@csteele thanks for your info, I got the ghost nodes removed and immediately I saw a change in my Z-Wave network speed, even deleting other nodes were faster after I deleted the node 2 of my mesh.
@bravenel Definitive the hub has something weird with ghost nodes, I'm not sure if this was corrected already but I deleted 4 GE dimmers after latest update 1.1.3.116 and they were there in the stick as ghost nodes, after I removed node 2, it took about 5 minutes, then everything else was faster.
Using Zensys I tested with my cloned stick first, I found ghost nodes 2,8,9,33,59 and 63. I removed them, everything was fine so I proceed to do the same on the HE stick, I noticed that node 8 was removed already by HE, I removed 2,9,33,59 and 63.
Right now everything looks stable, I will keep posting if I see something else.
Thanks
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Thank you for posting your troubleshooting steps! I am sure this information will be helpful to others.
I am glad to hear your Z-Wave network is behaving better now and that you'll be able to enjoy your Hubitat Elevation Hub! 
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Yesss, thank you, after Wednesday I will be away the house every day and I was a little stressed. 
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What would be good is for someone to do a separate writeup of a step by step guide on how to clear out ghost devices. (In a new thread). 
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When deleting a Z-Wave device, be sure to do an exclude on it. DO NOT FORCE DELETE. Doing that will leave the device on the stick.
What is the downside of leaving the device on the stick? I recently had my husband replace some of those old non-reporting z-wave dimmers with Lutron dimmers, and naturally I forgot to remove them beforehand.
Downside is that it can mess up your mesh. Those devices (nodes) may be in mesh routing tables in other devices. Best bet would be to power them up and do an exclude on them. Not doing this can cause problems.
They have been tossed in the trash for several weeks now, so no can do 
Why wouldn't a z-wave repair fix the problem?
The problem with excluding Z-Wave devices using HE is you don't always get a response that they have been excluded. Certainly in the early days anyway.
Because of this I've always used ST device exclusion to exclude devices from HE. I always get a response.
I then use HE to re-pair them.
It's much better now. I did exactly the same thing you did and usually go back in to delete the device in the Z-Wave info page prior to firmware .112. You can no longer do that.
I now leave a live logging open and try excluding the device. Will see it in live logging or look at the device list and hope it's gone from the list.
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The hub will automatically remove them after some time. That should clear up any issues.
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OK thanks.
Whew, thanks 
Reading through this because of the other thread about fixing the zwave mesh. So we really shouldn't need to use any other tools to fix "ghost" devices and the such? They will eventually clear up?
Interesting reads. I have installed ZenSy and can see that I have a defunct security node 69 which is causing issues. I can't remove it though. 
how did you determine that?
You can remove it, you must test it until it changes to dead.
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Look at your zwave list in Hubitat and then look at the list the nodes are showing.
