Depending on what you are using for the storage solution on your Hyper-V cluster, I would take a look at the error logs (both at the Hyper-V and SAN level). I'm not familiar with Hyper-V, but in other virtualization solutions (read: VMware), you can view log files and see where any disconnects or potential corruption is coming from.
The fact your guest VM(s) are being thrown into a read-only state, indicates there's an issue with Hyper-V talking to your SAN. I would double check your network links to each virtualization host, your Hyper-V "head" and the SAN.
I've seen this kind of thing happen before on REAL hardware before too. For what it's worth, you can't rule out physical links going down, but from what I've seen, it's usually an underlying driver issue. Basically, what happens is the file system is doing what it does...it starts getting backlogged due to write errors or cache errors and things start to unravel.
1. Read the Logs - I'd start by looking at system logs to try to isolate the problem.
2. Physical Storage Network Layer - You could be dealing with a SAN connection issue if your HBAs aren't on their latest firmware or if you're dealing with iSCSI, check network statistics to see if you have any evidence of problems there.
Another thing to consider is limited disk I/O. It's not uncommon in virtualized environments to carve up a 1-2TB LUN and connect 30 VMs to it... All it takes is hitting the threshold where there's too much chatter on the LUN and you've spent your disk I/O. the only solution is to get more spindles or switch to a block-level SAN solution with storage tiering or SSD.
3. Check HyperV and see if there are OTHER virtual storage adapters to use...or other drivers Ubuntu can use for virtualization. As I stated before, drivers are possibly a cause here. Some drivers and virtual hardware work better with virtualization simply because they are more patient and don't timeout as quickly. It's not uncommon for resource contention to cause slowdowns and some drivers give a good cushion to the disk...
4. Finally, look at your Ubuntu swap configuration. This may be something you can tune to take some load off the disk. You can possibly throw more ram and less swap at the system or check best practices...I've not played with HyperV much. I don't know all the sweet spots, but there are always caveats to virtualization and some work better than others with certain OSes. I have had no problems with VMware and linux....or VirtualBox and linux. (Red Hat, Cent, SuSE, and Ubuntu flavors)
