At 100MHz the MII(?) interface between the PHY and MAC will be clocked 10 times faster (the MII is the clock source). This might cause timing problems.
The flashing rx light probably means that the PHY is seeing the traffic.
A normal MAC unit (ie dedicated silicon) doesn't need to be told whether an interface is 10M or 100M - the PHY just clocks the data faster.
There will be a minimum input clock frequency to the MAC unit, which will be higher for 100M operation.
We've had problems with the SERDES interfaces (carrying 100M or 1G ethernet between extrenal devices (we nearly built a Ge switch!) with PLL internal frequencies exceeding limits (2.4G+ doesn't work well) when changing from 100M to 1G. You might have similar problems at lower speeds.