That's an odd problem. Do you only experience the increased idle speed when the fan is running? If the idle is always higher, I'd guess you have some kind of excess load on the system or resistance in your cables.
I ran an electric fan in my Sporty. But my system is totally revamped with dual batteries in the rear of the vehicle, long cables running both pos cables and a shared ground to the front, with an isolator separating the charging circuit between to each battery. So all of my cabling, to include the cable from alt to isolator is new. And I went with a thermal snap relay with brass temp probe through the radiator core below the upper radiator hose (inflow) to control the fan. So I'm not going to pretend to be knowledgeable about the SPAL controller. One thing that came to mind was a conversation I had with Everet a while back about the high output alternators. He mentioned something about them (or maybe just his) being of GM or some other make and that it required a "tickler wire" to provide a "stimulation voltage" for proper operation. Not sure it that's what you've got or if you've already got that covered. But I thought it was worth mentioning. I know my isolator has a post for that connection, which is why it came to mind.
Hope my babble wasn't too painful. I'm interested to hear what the issue turned out to be...
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1997 Sportage 4x4, auto-trans, Warn manual hubs, 4" UPYOURKIA front lift, TJ 106AA rear springs, 2-5/8" body lift, 31x10.50 treads, SmittyBilt SRC front and XRC rear bumper, swing-out tire mount, OBX LSD front diff, Track Finder rear locker, 5.38 R&Ps and... really crappy gas mileage! <img src="/forums/images/graemlins/shiner.gif" alt="" />