I recently had the same trouble, on my 22ft Commodore, with a 200hp Etech. Running a Lowrance HDS sounder combo
last week I moved the tranducer, which is on the port ( left ) side of the motor a little further away from the motor, approx 30cm from the motorand then lowered it so that the top of the transducer is approx. 1cm below the bottom of the boat.

tried it out Sunday morning and had complete success

I had an old boat I used to beach launch a lot - to save damaging the transducer we mounted it on a stainless slide attached to a piece of plywood and could move it along the transom and up and down on the slide for best reading using nothing more than speed clamps - just a thought you might want to try until you find the ideal location and depth below the hull

 What's it actually doing? Is there gaps in the Ocean floor as the boat picks up speed? Do you have the transducer cable sitting right alongside a power cable? What sort of transducer is it? And is there anything I front of the transducer on the hull? 

if it was mine it would be close to where those first holes are, then just depyh and angle.

its getting air from something then!

silicon a bit of marine ply on the transom and mount it to the wood, once you have it in the right spot, mark it and drill through into the transom, remove the ply and attach the transducer.

 Or turn your transducer around? It could be back to front! That knob on the front can't be to good for the air

This is ok Just wrong side of boat as you are doing put on starboard side.

Also be mind full of the fact that you only have a 6 mtr boat that is high in the water .Transom mounted tranys work better for bigger boats because they displace more water and there is more clean water under the boat ,you can only go up to a curtan speed with a 6 mtr boat before you will get dity water going under the hull ,bow down will generate more clean water to a point ,bow up will generate more dirty water at speed.

As far as the holes on the starboard side already I would tape the area off rub it back and put a layer of FLOWCOAT over and start again.

 Drill them to clean wood, allow to dry THOROUGHLY then use 24hr Araldite and a bit of timber dowel shaved down to a hammer- in fit. If they are only small screw holes, just spilt some jarrah down and whittle it to size. This is the correct fix for a hole in your transom if you want long-term results. If you can tap them in so they are recessed slightly you can finish over the top later.

I am currently camped on the beach at Ningaloo and have had nothing but issues with the new Elite-7. First it was the GPS issue mentioned in another thread, which turned out to be my UHF radio. That hgas been resolved by leaving the radio off. But the fishfinder side of things is ,frankly, crap. I mounted the x ducer as low down the vee as i could go, took great care with depth, etc, but results have been disappointing. Virtually  no picture at speed, and poor at low speed. Only fishing out to around 23 fathoms .I tried plugging the old Lowrance transducer in , from the LC 95-mt which was on the boat when i bought it, as that alway gave a good picture. Mounted on the opposite side further up the vee. Plugs are identical, selected generic 50/200 hz from the menu, and results were a lot better. No CHIRP, of course, or water temp, but bottom and fish were quite good. So it looks like I need to move the new xducer furher up the hull on that side. This will also stop it getting misaligned when the bottom drags on the sand. But I will have to wait until later in the week when the lower tides will clean the beach up, pull it out late afternoon, change and relaunch.

 Howdy guys,

I screwed it into the transome just to the right of the bung.

All of the old holes will be drilled, cleaned and bogged up, just want to place my sounder properly before I do the whole job, not just bits and pieces.

thanks for the info. I will take it out for a test tomorrow.

 It's not something silly like wrong kHz. Have you got it on shallow water or deep?

You have seen this,YES ?
http://fishwrecked.com/forums/fishing-essentials/soundergps-information-photos-reviews/raymarine-sounders
That transducer on yours looks different to the original ?