Ok I didn't quite see this same situation on another post so I thought I would describe my problem and hope for an answer.

I have an older model Emerald Cygnus tub: 4-person, ~140 gallons, 1-pump DS3 model (replaced in 06). I bought this tub used from a private owner only a few months ago. I transported it back to my home, ran the wiring and hooked it up and everything worked fine. Yay.
Two months or so of running fine I started having a few problems with the heater and upon further inspection found that the wiring to the heater has been shaken up a bit during transport and was now overheating and melting the insulation of the wires. All in all, heater went bad, replaced it, put new wiring and new electric panel mounting and everything went back to fine.

Now the current problem. I started having typcial Flo errors a week ago, so I of course checked the manual and did all of the typical troubleshooting actions. The filters were pretty old and dirty so I automatically assumed that was the problem and got new ones. However, replacing them didn't help, nor did running it without the filters at all. Also, all flow valves are open, no clog on water intake, and air has been bled from system. I guess I have to assume the the pump in general is just bad. The pump attempts to start every 10 minutes or so when it is on but just results in 10 seconds of very loud motor startup noise..(I don't know much about motors at all)..
Anyway before I call a service-man (expensive..) there is something very odd about the problem that makes me think there might be something else wrong. I have notice that if I shut off the power to the tub and let the water cool overnight down to the 50s - 60s, then turn on the tub again, the pump and heater come perfectly. No flo errors, no problem. I can set the thermostat up to 102 or whatever, and the pump will continue to run until it heats the water to the set point and deactivate normally. However once the water gets warm (above 80 degrees or so) and the pump shuts down, that is when it won't come back on and I get my flow error. Why would a pump work fine with 50 degree water, but not with 90?
I've tested this serveral times, and every time I leave it off overnight and try in the next day it works perfectly until it gets warm and shuts off...
I hope someone who reads this (and knows much more about mechanical stuff than I do) can throw out some ideas as to why this could happen.
I'll check back regularly and reply as best I can to any questions.

Does it always do this after it gets hot?

Yes it does. The warmer the water, the more the pump struggles to come on. I've tested it several times around 83 degrees and it has never worked then. I actually turned the power back on today and it read 77 so I tried to start it and the pump struggled for 5 seconds or so but then started up and heated the tub to the 100 degree point I set. Aften then, no more luck.

I also did some more probing around today including disconnecting the pump and playing around with it. I found that it had a bit of resistence to spinning so I'm thinking maybe one of the bearings is out. A friend also suggested testing the capacitors. I'm not sure if either of these could be temperature related or not, but I plan on testing/replacing them in the next day or two.
I'll try out any other suggestions posted as well and post anything else I learn up here.

Yes they can be temp dependent. If you can get that motor to a shop, have them replace the bearings and start/run capacitors.

ok. just got the motor back from being serviced. they said it looked pretty rough and replaced the capacitors and the bearings. I put the motor back in the tub and it works so far. The water was around 60 degrees when it first turned on. When the water was around 85, I turned it off to test it again and it worked great then to. It's also much quiter now.

One new problem though. Seems like some of the wiring got messed up at some point.. When the motor turns on, it seems to be in high speed mode. The indicator on the hot tub says its on low speed though. When the jets button is pressed, the hot tub indicator show high jets, and the motor turns off. When I go back to low speed, the motor turn back on fine, but again seems to be in high speed mode (decided that from the power of the jets in the hot tub). So the motor is on high when the tub says to be on low, and when the tub says go to high speed, the motor is just confused.

Not sure if this is a problem with the motor though. Might be more the wiring in the control box of the time (i had to move the box around alot when taking the motor out and putting it back in, something could have been messed up).

I plan on researching the problem a little and trying to figure out/fix whatever the cause is. Just wanted to update on my current situation.
All in all, it works much better now, and I can start getting back in and enjoying it. YAY.

You need to be absolutely certain that your common - white wire is on the pump common terminal.

Red/Black on the high and low.

Take the motor cover off and verify this - do not guess at it.

I checked the wiring to the pump and the guy at the motor shop wired it back incorrectly. Had some switched around so the pump ran on high when the hot tub controller wanted it on low. Anyway, i fixed the wiring and it seems everything is running smoothly and quietly now, so I hope the motor wasn't hurt from the error.

All seems well now. Thanks Pageup for the advice and working with me to figure out the problem! Hopefully someone else will find this information useful as well. Don't forget, check the motor when the people are done servicing it...