We have two AC units/zones servicing our house... We have both systems set (at the thermostat) to continuously run the blowers even if the compressor has cycled off. The blower on one unit, however, cycles off briefly for about 2 seconds when the air conditioner compressor turns off, despite being set to run continuously. The other unit does not do this. Any ideas why this may be happening?

Very common in modern furnaces to change blower speed when A/C starts.

We have two AC units/zones servicing our house... We have both systems set (at the thermostat) to continously run the blowers even if the compressor has cycled off. The blower on one unit, however, cycles off briefly for about 2 seconds when the air conditioner compressor turns off, despite being set to run continously. The other unit does not do this. Any ideas why this may be happening?
Yes, but since one runs straight along without such suttering, could one be wired incorrectly or could the thermostat be faulty?

Are they Identical furnaces? Does one use the same fan speed for fan and cool. One may have high speed for cool and med/low for fan, where as the other furnace uses med/high for both fan and cool speed.

What NorthernHeat said is correct, the furnace that shuts off for two seconds may be set to run on a different speed during fan only operation then A/C operation, normally this information is in the installation instructions of the furnace . If you do not have this booklet , it could be down loaded from manufacturer web page or acquired from your local A/C contractor.
The other furnace may be set to operate at the same fan speed as the A/C.
This feature is only available on some of the newer furnaces. Mike