For some reason if I copy files from one folder to another in this case JPEG images and try to convert them to PNG in the new folder location using the command image CONVERT=PNG they convert fine but show up in the source folder and not in the place that I copied them to, any ideas? (Right is source, left is Destination)
You need to make sure that the target (left) is changed to source before you convert. Unless you did something to change source/target then what you are seeing is expected.
What's the full command you are running?
I also can't see anything appearing in the source folder in your gif, while files are appearing in the destination folder. This question is confusing me if the gif represents what is happening. 
The right is not the source if you just clicked in it, unless you changed the source back to the right just before running the command, which we cannot see due to the way the gif is cropped. Showing the whole window would be better than this cropped view, unless there is some reason you cannot do that... ... ... hmm.
Made a mistake my bad, the left is the destination folder, the right is the source, and the full command is image CONVERT=PNG not sure how I forgot to include the image part at the start of the command (It's 4AM) also side note, it converts to the right place if I use the convert window instead of the command, though I'm still curious as to why it would do this using the command.
The gif shows files being selected on the left before the command is run, and files then appearing on the right.
It looks like the left is the source, and the converted files appear on the right, which is the destination?
If so, that is what should happen when the image convert=png command.
If you click on a side, it normally becomes the source. The source/dest isn't left->right; it's the active side to the inactive side.
Use image convert=png here if you want to convert the images from the source (active) folder into the source (active) folder.
image convert=png here was a good solution to the problem, but just as an aside, even if I have the two folders open in two windows the files I copied still convert to the folder I copied them from. It's not the first time I noticed them, when I have converted them before I've had it not show anything only to look back into the source folder and seeing the files.
Image Convert=xyz, wittout the here, will take files from the source and write them to the destination. The same as is happening in your gif, above.