I'm having the same issue after a reboot. I go into the Web UI and it says the storage pool is running, but it does not show up in explorer. The network shares are visible, but if I try to access any of them I'm told that the device is not ready. If I stop the pool and then restart it the pool drive is now visible and the network shares work. I am not seeing any other errors. I previously had the 9-21-15-r2 version installed and I noticed the same behavior. I have run UserMode.cmd and rebooted and that didn't change the symptoms.
1. What OS? WHS 2011
2. Do/did you have a Paragon product install/ed? No
3. What disk tool you have installed (Acronis and others)? Hard Disk Sentinel
Here is a section of the Flexraid.sys.log that shows the only error I'm seeing. The log starts at 22:48 after a reboot. At 22:53 I restarted the pool which then was visible and useable.
[2015-10-03 22:48:06.270176][3544][DLL_THREAD_ATTACH] ID=3544
[2015-10-03 22:48:21.684843][3780]Build Timestamp [Sep 21 2015 08:31:40]
[2015-10-03 22:48:21.684843][3780]
--------------- Storage Pool Start ---------------
[2015-10-03 22:48:21.684843][3780][Mounting Storage Pool]
[2015-10-03 22:48:21.684843][3780][VM already acquired...]
[2015-10-03 22:48:21.684843][3780][Building options...]
[2015-10-03 22:49:10.978312][3780][mount] [Create New Storage Pool] ErrorCode=31 Message=Mount error! Code=1359 Message=An internal error occurred.
[2015-10-03 22:53:31.795009][6220]Unmounting the storage pool
[2015-10-03 22:53:53.748936][6556]Build Timestamp [Sep 21 2015 08:31:40]
[2015-10-03 22:53:53.748936][6556]
--------------- Storage Pool Start ---------------
[2015-10-03 22:53:53.749936][6556][Mounting Storage Pool]
[2015-10-03 22:53:53.749936][6556][VM already acquired...]
[2015-10-03 22:53:53.749936][6556][Building options...]
Here is part of Flexraid.log:
[2015-10-03 22:47:14,786] INFO : Setting core service port to 9595
[2015-10-03 22:47:14,802] INFO : Setting Http port to 8080
[2015-10-03 22:47:14,802] INFO : Https port not set. Https requests will not be serviced...
[2015-10-03 22:47:14,927] INFO : Starting FlexRAID...
[2015-10-03 22:47:14,927] INFO : FlexRAID 2.1 [Snapshot 1.1 / Storage Pool 2.0] [2015.09.25]
[2015-10-03 22:47:14,942] INFO : Started: October 3, 2015 10:47:14 PM PDT
[2015-10-03 22:48:16,760] INFO : Initiating FlexRAID Storage Pool...
[2015-10-03 22:48:19,640] INFO : Host OS = Microsoft Windows [Version 6.1.7601]
[2015-10-03 22:48:19,640] INFO : Building View Registry...
[2015-10-03 22:48:19,718] INFO : Building Auto View Registry...
[2015-10-03 22:48:20,358] INFO : Loading View options...
[2015-10-03 22:48:20,686] INFO : Using Auto-View definition...
[2015-10-03 22:48:20,686] INFO : Building View Handler...
[2015-10-03 22:48:21,668] INFO : Mounting Storage Pool drive...
[2015-10-03 22:48:39,883] INFO : Reconnecting Documents="D:\ServerFolders\Documents" /GRANT:Everyone,FULL
[2015-10-03 22:48:45,808] INFO : Reconnecting Music="D:\ServerFolders\Music" /GRANT:Everyone,READ
[2015-10-03 22:48:46,813] INFO : Reconnecting Pictures="D:\ServerFolders\Pictures" /GRANT:Everyone,READ
.
.
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[2015-10-03 22:48:49,761] INFO : Reconnecting Temp="D:\Temp" /GRANT:John,FULL
[2015-10-03 22:53:31,793] INFO : Unmounting View...
[2015-10-03 22:53:31,794] INFO : Unmounting View complete...
[2015-10-03 22:53:53,321] INFO : Initiating FlexRAID Storage Pool...
[2015-10-03 22:53:53,415] INFO : Host OS = Microsoft Windows [Version 6.1.7601]
[2015-10-03 22:53:53,415] INFO : Building View Registry...
[2015-10-03 22:53:53,416] INFO : Building Auto View Registry...
[2015-10-03 22:53:53,433] INFO : Loading View options...
[2015-10-03 22:53:53,470] INFO : Using Auto-View definition...
[2015-10-03 22:53:53,470] INFO : Building View Handler...
[2015-10-03 22:53:53,748] INFO : Mounting Storage Pool drive...
I hope this helps!