Question on disc drive encoder

I'm having a problem with my 7900 I'm trying to get up and running that I wanted to bounce off the folks here. When you hit the load switch, after spinup the heads seek cylinder 0 and rest there (and an interrupt is sent to the cpu). However, any command sent to the drive via diagnostics causes the heads to slowly step out one cylinder at a time to the innermost track. Then the cpu gets a "no command flag" message which basically means the cpu never got acknowledgement back This makes me suspect the encoder mechanism. The drive uses an IR emitter/detector through a glass reticule with sector markings on it. But if the encoder was shot, wouldn't that make it hard for the drive to initially seek cylinder 0 upon loading as it does correctly? Just curious... more of a philosophical question than a need for direction... Thanks in advance! Jay West