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I finally got my Jimny back yesterday, after more than a month at the garage.
The Suzuki dealer took out the gearbox and couriered it to a transmission specialist, then put it back in and tested it. That cost me £240.
The transmission place stripped the gearbox and replaced a set of bearings, then sent it back to the dealer. That cost me £340
Total cost to me nearly £600
The transmission place had another Jimny in with exactly the same problem last month. So it seems it's quite a common fault. Mine is on 05 reg with 40k miles.
Did your gearbox had any signs of oil leaking ? I've read lots of posts regarding a faulty gearbox oil seal (from the factory), which is quite tricky to properly replace.
Our 2006 VVT Jimny gearbox bearing totally disintegrated causing the gears to jump and mash teeth. Cost AU$2200 to repair with genuine parts. Was leaking oil afterwards, when I took it back for fixing the gearbox guy showed me how to replace the main input seal, the entire gearbox needs to be split. Pre-VVT has a 4 bolt plate to access it.
Pic of the main input on VVT Jimny, note there are no bolts around it.
Just had a similar problem on my 2008 Jimny 1.3 JLX+ Auto. Dealer says it is a "known" problem but not a recall issue. Symptoms were a slight whining noise when accelerating up a gradient at about 35-40mph. They had the gearbox out and "replaced the gear transfer". They removed and stripped the transfer box fitted new gears and rebuilt it. Fortunately, it was in the last month of warranty so I didn't have to pay for it. I gather it is about £250 parts and £400-£500 labour if you have to pay for it. Also had to pay for new front disks and pads at only 9,000 miles which was not covered under the warranty as Suzuki says it was "fair wear and tear". I hope the disks last longer than 9k this time!
