An alternative explanation is that the operation is programmed to gear limiting speed, and so the handle is down, but the gear doesn't extend until a lower IAS is reached, then it deploys as demanded.
Assuming that the command itself and the switch/button is OK, then check that the gear operation for that particular aircraft isn't set for Off-UP-Off-Down, instead of the usual `toggle` gear up/gear down.
The intermediate step is used by several addons to create a more realistic operation of the gear lever, where it is returned to the median position after use. Usually this can be checked simply by looking at the lever in the VC.
If it is, then you may find you have to press the button not once but TWICE to get it to return to the median.