Sorry to as the dumb questions but I just want to clarify what the problem is.
You have an array with two 1GB links connected on the active controller, your hosts have multiple 1GB ( how many?) links connected to the switching.
You are seeing a 100MB/s limit on IOMeter running within a single VM.
You say for the array "The combined throughput of both ethernet adapters can never exceed 1Gbit/s"
So for a single 1 gigabit link the maximum theoritical throughput is 108 megabytes per second.
If you have two separate VM's running on two separate hosts running I/O meter you are seeing 50MB/s throughput on each?