I had the same intermitent Climate Control behaviour on my '98 M3. I followed the procedure in the URL noted in this thread and am pleased to report it seems to have corrected my problems.
I followed the procedure pretty much exactly as described although I removed the Business Radio to get the climate control unit out. I did this because the sunglass section referred to in the link is filled by the SMG controls and this makes getting the Multi Function Display difficult to get out.
I'm not much of a soldering kind of guy, so rather than attempt this myself, I printed the instruction out and took them to a local electrical repairer who changed the capacitor in 5 minutes while I waited.
Total cost AUD$10 and 1 hour of my time. Only additional tool required for my approach was a hex key to get the Busines Radio out. Completely straight forward and little risk from my experience.
Full marks to Richard, his detailed naration saved me some significant $$$....