Is the Ubuntu VM's / on a fixed or dynamic VHD? The former provides (modulo filesystem fragmentation) linear addressing of virtual LBAs to physical LBAs, and the latter can be heavily fragmented and result in sequential read/write operations becoming random access, which on a HDD kills performance.

My advice for anyone running VMs is if they're on HDDs or they're highly tuned for disk usage (databases for example), use fixed VHDs, otherwise use dynamic.