Forget rar2zip, just get WinRar.
Install Winrar, which will install some options for when you right click on files/folders.
Then go to your rom directory, and select all the rom rar archives. (CTRL-A will select all the files in a folder). Right Click with the mouse, and select "Extract each archive to seperate folder"
Once done, select all the folders you have just recreated, Right click and select "Add to Archive...." to pop up the WinRar dialog.
Select ZIP for archive format, select your desired compression method, click on the "File" tab and then tick "Put each file to seperate Archive" option.
Hit go - and WinRar will create a Zip for each rom folder, with the correct name intact.
NB this will leave you with all the rar and zip files, so you may want to remove the rar files once done.