Query - if I leave the main power supply for the windlass and the bow thruster in the "on" position without operating either of them, does it drain power from the batteries even in standby?

It should not. (Although relays could take a little standby current)

Maybe I should only activate the power supply for these two power hungry items right before I need them?

That's wise, just in case either is switched-on unwittingly.

The symptom does seem like a massive power drain, suggesting that the switchgear for your bow thruster needs urgent attention.

 

Sounds like you may have a poor DC ground somewhere in your system. Basically, when you powered up the thruster the ground for the instruments and fan was brought up to a greater than 0 volt level. This makes it appear like they lost power but in reality the ground from your thruster was not able to dump the electrons into the water fast enough. Double check all of the ground connections on your thruster and windlass, make sure they are not corroded and tight. Make sure the wire is of a sufficient gauge.

Of course, like all electrical problems, there could be other explanations. I one time had a similar problem with the taillights on a car - once I rewired the ground the function returned to normal.

 

Frog reminds me that checking the battery terminals for good contact might be a good idea too.

 

Quick question: Is there a separate battery for the Bow Thruster and windlass? Given their high current draw and distance from the house battery banks, they're often installed with a separate battery. If you're turning the systems off, are you still charging that separate battery? If not, that may be the problem. Waiting a few minutes and shutting off all the other electronics may have allowed the house batteries to charge the windlass/bow thruster batteries enough for them to work properly for the short time needed.

 

The boat has a starting battery for the engine, and two house batteries which are located under the aft bunk. There is not a separate battery for the windlass and bow thruster.
Thanks to the responses I will be checking the battery connections and the connection to ground to be sure they have good contact. Thank you for all the information - as a beginner I need it!

 

Frog:
You were right on the money. Spent Saturday working on cleaning elictrical contacts. Started by cleaning the main ground to the engine block but still no good. Then I moved up to cleaning the terminals on the starting battery (corroded) and the two large house batteries (badly corroded) and all wire attachments to all batteries. Guess what - everything works perfectly now. Thanks for the heads up - probably saved a bunch of $$ by doing it myself.