[hlbjtm72]

I have a 99 beetle the trans was working fine no slipping was running like it should started having some electrical issues like alarms and settings started coming on that never had before. Went out to go to work trans won't go past second, took it to a shop they tried to put it on 3 different machines nothing came up its been a month since then I had to go to the store was in second gear and all of a sudden the car made a weird noise and trans now switching gears fine again and it made a weird clicking noise when I stuck my key in ignition. Is it my transmission or is something else going on

 

[D2Beetle]

At this point you need to get it scanned by the VW dealer or someone with VCDS (aka Vag-Com); some aftermarket scanners in use at your local mechanic shop will not pick up some/all transmission codes.

Off the top of my head, it sounds like your transmission is going in and out of "Limp Mode"; which might be the result of a malfunctioning valve body.