So if you haven't changed the front chainring, and you're sure the chain is the right length for your bike and is not damaged. Then make sure your Rear Axle is tightened properly so your wheel is in proper alignment (Shimano Hexle recommended 5 Nm torque).
Then if you are still experiencing a chain that is hanging / catching in certain spots on the rear cassette when you turn the cranks, then your going to want to make sure your Rear Derailleur hanger is straight / not bent. A hanger can be bent pretty easily in a crash, or if your bike falls over onto the rear derailleur or if a stick gets caught in the chain while pedalling.
You may not realize that your hanger is bent just by looking at it, even if it's off just a few Millimeters it could cause shifting issues, such as the chain catching on the rear cassette teeth at certain spots as the chain comes out of alignment due to the hanger being bent. To fix this either replace the derailleur hanger (usually about $15) which is specific to your bike, or get the Park Tool DAG-2.2 Derailleur Hanger Alignment Gauge which will determine if the hanger is out of alignment and allow you to bend it so the derailleur is straight. See How to Align a Derailleur Hanger Using the DAG-2.2. A hanger that is out of alignment by just 3mm can cause shifting to be off by 0.5mm. If it's rebent into position it will improve shifting.
NOTE: Even after you align the hanger, your chain may still skip or catch while spinning the cranks while your bike is still in a work stand, but if you take it out for a short ride, you may find that your problem is solved and the shifting is much better.
Lastly, if the hanger was not bent or out of alignment, it may be the Rear Derailleur cage that is bent, which may need to be slightly bent back or you may need to replace the derailleur. However, it's far more likely that if you had a crash or set your bike down on the rear derailleur that you'll bend the Hanger before you'll bend the rear derailleur.