Micro-balling can be attributed to the print process, placement process, reflow process, the environment or the solder paste itself.
Verify solder paste is properly stored, and allowed to sufficiently warm to ambient temperature prior to being used. Verify proper stencil design guidelines have been followed, especially stencil thickness and aperture size, and verify deposition registration is accurate and repeatable. Verify that the reflow process parameters; (especially the first two minutes) are correct for the solder paste being used.
Too low of a rate-of-rise will contribute to micro-balling by allowing the solder paste to hot-slump. High-humidity, and high-temperature environments can contribute to the cold slump characteristics of solder paste. If boards are being printed and allowed to sit for an extended period of time prior to placement and reflow, cold-slump could be a contributing factor.
Consider evaluating a solder paste with a slightly higher viscosity and/or metal load. This will help combat the affects of both cold and hot slump. Check placement pressures to verify components are not being driven too far into the paste deposit.