I had the exact same problem, ended up being the cassette being worn on few middle to larger gears on the rear.
One thing I can say is, that your chain is definitely too short at the minute, put at least another 2 links in (1 inner outter)
Btw I hope you followed Shimanos instructions on breaking and rejoining the chain. Or else you could have some difficulties being stranded with a broken chain soon. Seen it happen so many times on club rides.
I had the exact same problem, ended up being the cassette being worn on few middle to larger gears on the rear.
One thing I can say is, that your chain is definitely too short at the minute, put at least another 2 links in (1 inner outter)
Btw I hope you followed Shimanos instructions on breaking and rejoining the chain. Or else you could have some difficulties being stranded with a broken chain soon. Seen it happen so many times on club rides.