I know this thread is old but as the problem wasn't solved, I wanted to share a solution that I found. Maybe it will help somebody else avoid all the time I wasted on it.
I had a similar problem with my jrok encoder to what the thread starter described. I purchased a jrok sync cleaner but it didn't solve the issue. The image had a lot of interference and looked terrible from both S-video and component.
After tripple-checking my wiring etc, I purchased an extron rgb interface for $9 off ebay. These devices are designed to clean and process rgb sync (as well as other things). Anyway, the image is now perfect and I get the added benefit of gaining horizontal and vertical shift controls which the jrok lacks. This is helpful because some sources, like neo geo games, always seem to be shifted to the left or right and this is annoying to fix on a tv (without going into the service menu every time I change games).
The extron rgb interfaces can also combine seperate horizontal and vertical sync into composite sync (which the jrok needs), or do the reverse (as well as sync on green).
If I was doing it again, I would not have bothered purchasing the jrok sync cleaner as it doesn't do a proper job on all rgb sources. It may be fine for jamma boards but it seems to struggle with other sources. It also needs a seperate power supply which isn't provided (just like the jrok encoder).
The extron rgb interfaces can be purchased for the same price as the jrok sync cleaner these days and they are a better purchase. You get perfectly clean composite or seperate sync from any rgb or vga source and image shift controls for between $5 and $25. The jrok sync cleaner will not combine seperate sync so it is useless for many non-jamma sources.
I am using it with an arcade vga which puts out seperate sync. You are meant to be able to combine v and h sync from an arcade vga by just twisting the wires together but the resulting signal is too dirty for the jrok sync cleaner to fix completely. My guess is that this was the source of my interference. The other potential source was me using the same 5v psu to power the jrok encoder and the sync cleaner. The extron interface has its own power supply so this is no longer an issue. The starter of this thread was using a neo geo as the source so perhaps the jrok sync cleaner is only good for jamma pcb's. All the other suggested solutions involved soldering resistors to the wires (which I can't be bothered for) and nobody followed up to state if this even fixes the issue.
Based on my experiments, if you get a stable image and interference is the only issue, then your wiring is probably correct and the jrok sync cleaner is just not suitable for your source. When my wiring is wrong, I typically get no image or a rolling image plus innacurate colors.
You will need male BNC connectors for the output from the interface which cost me another $10 but it was worth it. The interface has a built in vga cable for the input so if your source is not an arcade vga, you may need to make your own rgb to vga cable to connect your device. For a neo geo, a scart to vga adapter would be fine, or a custom cable modd / breakout board.
The image quality through s-video from the jrok is excellent btw. It is a great solution for using a US CRT tv as an arcade monitor for mame emulators etc. The main problem is that they are a lot of work for non-technical people like me to hook up. You have to find /make your own 5v power supply and make your own rgb cable as they have no vga or scart input. If soldering isn't your thing, I highly recommend a vga breakout board. These allow wires to be connected into numbered screw connectors, instead of cutting open an existing vga cable and guessing what all of the wires do when there is no standard for wire colors etc.
The extron rgb interface makes wiring it up a lot easier because the output is already broken down into rgb and sync wires. You just need to pull ground off one of the rgb wires but that is easy if you use a vga breakout bread plus a male bnc to male vga cable. My vga breakout board was $9.
As there are very few (if any) consumer ready rgb to s-video encoders that don't change the resolution, the extron interfaces and vga breakout boards paired with a jrok encoder, are good solution for people who are not comfortable with a soldering iron and dont want to spend a fortune. Almost every other vga to s-video device is a scan converter which changes all output to 480i which defeats the purpose of using an arcade vga card.
As someone who used to live in the UK with an rgb scart tv, I can say that the component output from the jrok is almost identical to rgb and therefore a great option for gaming on a large crt tv instead of buying one of those tiny Sony PVM rgb monitors (which don't look like real arcade monitors).
