At 108,000 miles our Fabia 1.9 diesel started crunching when changing from 1st to 2nd and I assumed the worst.... New synchro at the very least. We've had it for 15 years, it's had 2 learners try to kill it and one even tried to engage 1st gear at 40mph so I assumed it was toast! Not so. I was told by a local garage that these gearboxes hardly ever fail so they changed the oil for modern synthetic and bingo. It's as if it has a replacement gearbox now! Might be worth trying if anyone out there has this problem..... 

What gear oil you bought? Brand, viscosity? When I bought my fabia 1.9 TDI vrs I changed fluids. Gear box oil got changed using Castrol oil finder due to slightly poor shifting between 1st to 2nd and it was worse changing on cold starts. Same shifting behaviour when warmed up. I went to dealer and bought 6 speed gear oil they listed. Didn't improve on what it was like before trying Castrol gear oil, but better than synthetic Castrol oil. 

 

Changing the engine mount to polybush helped gear changes - less movement of engine.

 

So I'm skeptical. Is your car 5 or 6 speed?

 

 

All this is caused by low gearbox oil level, changing the oil is no better than topping it up, the problem is after a while actual wear happens due to lack of lubricant, at which point topping up can only arrest the wear.

In my case, the gear oil was full and you wouldn't notice any gear change problems. 

 

Just thought I'd caution about putting 'any' gear oil in.