Last thursday night my idiot of a manager put an old very used PTR cleaner on our only print of Tomb Raider. upon seeing this I questioned his judgement and was told that the companies head engineer told him that the reason that we have had problems with prints going in and out of focus... is because and get this... The prints are dirty.
Plus as a laughable side note. We are sitting down watch Tomb Raider and the DTS trailer doesn't kick in. So I run upstairs and check it out. A disk is in the B drive and vise versa, also the print was not threaded through the DTS reader.
Calgone take me away 
It doesn't matter which dts disc goes in which drive. I make it a practice to use drives A and C because the B drive is the most difficult one to get to when it dies and must be changed out. Also using A and C drives keep the drawers side by side, which is nice.
It's very unlikely that dirt would have any effect on focus stability, unless it built up in the gate and affected gate tension.
Any good film cleaner (PTR or web cleaner with FilmGuard) should be able to effectively remove any random loose dirt picked up in previous handling or projection. If the "old very used PTR" has hardened, it will not have enough "stickiness" to effectively remove dirt particles.
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John P. Pytlak, Senior Technical Specialist
Worldwide Technical Services, Entertainment Imaging
Eastman Kodak Company
Research Labs, Building 69, Room 7419
Rochester, New York, 14650-1922 USA
Tel: 716-477-5325 Cell: 716-781-4036 Fax: 716-722-7243
E-Mail: john.pytlak@kodak.com
Web site: http://www.kodak.com/go/motion
-Mike