As you can see from the shot below I get exactly the same problem you describe with the default Goose on the water runway at Orillia "Lake St. John".
This area of the lake looks like water but FSX treats it as a hard surface & the Goose will take off quite happily with the gear down as if it was on a hard runway.
However, if you slew or taxi the aircraft into a "deeper" part of the lake you can raise the gear & take off in the usual way.
To confirm my findings I tried it with the FSX default Beaver floatplane. When it first loads on the water runway (Rwy 31) it won't move but again, if you slew it into "deeper" water it behaves normally.
This indicates that the fault is not with the payware aircraft but with the Orillia scenery.
I found another bug after taking off. The Beaver moored at the pier is resting on the bottom of the lake.
I assume there is a conflict with some areas of the lake & the terrain. If it concerns you I suggest you contact the developers of the Flight Ontario scenery to see if they have a fix for it.
