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2006 Seadoo Challenger 1800 thumping

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Alright folks,

I am new to the Seadoo jetboat world and I am hoping to get some help/advice so that I may be able to help someone on this forum in the future. Sorry for the longer post but here's the situation..

Bought the boat before the winter and it ran fine, I winterized it and all of that good stuff. A few weeks ago I take it out for the first time and everything runs great at first. 5 minutes after cruising down the river I stopped and idled around for a little to check things out. Then when I rolled on the throttle, at low speed and RPMs there is this loud thumping coming from the engine compartment. That it the best way to explain it. When I jammed on the throttle it would run perfectly fine and get on plane with no issues/noises or anything. It runs fine at WOT or when you jam on the throttle. It only does it at low speeds/RPMs/rolling on the throttle. When I opened up the engine compartment it looked like the entire engine and pump shook every time it did it. I can't pin point where it is coming from but it almost sounds like a gear or clutch slipping/skipping.

Fast forward to the next trip out and I have the same issues.

Before the third trip out I pulled the pump and inspected everything (the impeller and wear ring were replaced right before I got it along with a supercharger rebuild). Splines all looked good and nothing seemed out of sorts. So back to the water I go. Once again right off the dock I rolled on the throttle and no issues, gets on plane, cruises great. Then after its warmed up it would start to make the noise/thumping again.

Summary: The engine idles fine, and runs WOT fine. It also runs great when it's just getting warmed up. Then it starts to make a thumping/slipping noise once warmed up and only when rolling on the throttle and at low RPM ranges (I don't want to use the word knock because I'm a fairly mechanically inclined type of guy and I do not believe it's an engine knock). For reference the thumping will happen every 1-2 seconds.

Anyone else have this issue or have suggestions?
 
Could there be some slop in the deflectors and at lower RPM one is caught up in a vortex and banging up and down a little??
 
Hey Wicked, have you had any luck with this one? Did you ever get your boat into your mechanic?

I've had mine out a couple times since I pulled the weeds off the impeller shaft and, knock on wood, it hasn't made that noise again.
 
It’s actually still at the shop. It needed a new DESS post which is taking a few days to get in. Other than that there were a couple random occurrence codes thrown so he investigated all of them and they all checked out OK. Basically I’m waiting to get in back (should be within a week). And then get it out on the water to test again. I will update when I find out!
 
Little update today. Finally got it back from the shop. They did the normal seadoo service stuff, read/cleared/investigated a couple occurrence codes, ordered and installed a new DESS post, and ensured me everything looked and ran great. So I took it out on the water immediately after picking it up and it still makes the noise. It also now bogs down completely and barely even has any throttle or acceleration. It will idle great but it’s almost as if it is getting no fuel at all. I’m wondering if the noise is backfires and a possible bad fuel pump is causing this issue? Anyone know how their challenger acts with bad injectors or fuel pump?
 
Latest and greatest. Got it back to the shop and everything checked out. Fuel pressure was good and not throwing any codes. The mechanic took it out on the water and it acted up so he disconnected the air hose line that goes into the air box and it ran like a dream. It still pops a little but we think the injectors were dirty and still need to be cleaned out a little. So I took it out on the lake this weekend and it ran pretty bad at first so then I disconnected the air hose and ran it ran fine again. I am wondering if that air box is a little plugged up and causing airflow issues? Also I may replace the injectors just for good measure.
 
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