A colleague of mine has posted a great article on one cause of these errors. Turns out there are specific refreshers that can be targeted providing WinRM and SCVMM the extra time needed to complete the job. Be sure to read the entire article carefully as there are implications with upgrading to SCVMM 2008 R2. Great article Robert!
Error in SCVMM
A Hardware Management error has occurred trying to contact server <your host name comes here>.
(Unknown error (0x80338029))
As it turned out, during refresh we did not wait long enough for a wsman response. The operation that timed out was to enumerate the SAN LUNs.
In SCVMM 2008 this timeout is 120 seconds by default. Fortunately, we can increase this timeout to a maximum of 300 seconds.
Read the entire article:
SCVMM 2008 Error (2927) A Hardware Management error has occurred trying to contact server