Why was I getting an uncomfortable feeling in an R22 at 3,000 feet?
Typical height for helicopters is 500-1,500 AGL, and almost all flights are conducted in this regime. 

Below 1,500 AGL the surface is quite close and the ground moves by fairly quickly, so you have a good point of reference. 

At 3,000 AGL, you can feel quite disconnected from the earth and can have a bout of altitude fear. 

When I had to circle up above out of a valley airport in an airplane, with minimum VFR visibility due to smoke, I felt like I had to keep cross-checking my instruments to maintain airspeed and bank angle. It was an uncomfortable feeling, even having had lots of hood time and actual IMC. So its not unusual for unusual flight regimes to have an unsettling effect.

The circling could have also cause some disorientation.  

The most important thing, which you accomplished, is recognizing the signs, not panicking, and you kept flying.