How To Use a Commuter Check Card to Purchase a Caltrain Monthly Pass

Warning
Before I start, let me recommend that you don’t try this. The potential savings you gain from using pre-tax Commuter Check cards likely won’t be worth the pain of actually trying to buy something with them. Return the cards to your employer and ask them to enroll in another option for funding your commute costs pre-tax!
Update: The Autoload program via Clipper works great. Instead of buying a pass in person with a commuter check card, you tag on/off once at the beginning of the month to load a new pass.
Goal
****Use two Commuter Check cards issued by an employer (each containing $100) to purchase a zone 1-3 monthly Caltrain pass on a Clipper card (for $179).
What Not To Do (Because It Doesn’t Work)
This section is intended to lower your expectations to the appropriate level. Almost all advice I have received on this topic has been either been out of date or blatantly incorrect, resulting in more wasted time than I ever thought possible. Please take my own advice with a grain of salt, as anything related to Caltrain or Commuter Cards is likely to change in unpredictable ways in the near future.
Walgreens
Since monthly Caltrain passes are usually purchased at Walgreens, this is a common first stop when trying to achieve the goal listed above. Unfortunately, although Commuter Check cards are labeled as credit card compatible, they dont work in the standard machines and cannot be accepted by Walgreens. This fact does not stop most Caltrain/Clipper/Commuter Check employees and random people on the street from suggesting this option every time you ask.
Online / Over the Phone
For some reason, probably related to the same reason Walgreens can’t accept them, Clipper’s online system does not accept Commuter Check cards. Again, this fact does not stop Clipper/Commuter Check call center employees from suggesting this option every time you ask. The Clipper call center will even try to process your Commuter Check card and tell you there is something wrong with it. This will result in you sepending another 20 minutes on hold with Commuter Check customer service just to be told that the card is fine and that you should purchase your monthly pass online (see beginning of this section).
In Person
Explaining all of this to a Clipper call center employee will sometimes result in them telling you that you can only use your Commuter Check cards at a Caltrain booth with a clerk (real person). In my case, they strongly suggested I go to the 4th/King Caltrain station before 7pm. While this advice is getting closer to the right answer, if you actually try going to 4th/King and asking around for a clerk or a booth, you’ll eventually discover that all of the Caltrain clerks in the entire system were laid off a few months ago. The remaining employees at the station fall back to the commonly issued advice above (see Walgreens & Online / Over the Phone).
What Does Work (Sort Of)

I’d like to credit the clerk at the Walgreens across from the 4th/King Caltrain station with the first halfway useful advice. Apparently, the Transit Store at the Powell street BART station accepts Commuter Check cards in exchange for Caltrain monthly passes!
BART Transit Store
Amazingly, the magazine stand style booths at some of the major BART stations along market do take Commuter Check cards. Unfortunately, some open late / close early and asking a BART employee for their hours results in very inaccurate information. Also, for some reason the Civic Center booth (where I was advised to go because it opens earlier than most others), does not take Commuter Check cards (anymore). Where can you use them? Based on my experience,** I know for sure that you can use them at the Embarcadero BART station Transit Store booth** and should be able to use them at the Powell street station if you can get there when they are open.
Bad Cards
When I finally reached a person with the ability to accept Commuter Check cards, I found out that one of my two cards was “malfunctioning.” According to the clerk, this happens all the time. I happily paid the remainder of my monthly pass with my own credit card in order to end the whole painful ordeal! I returned the bad card to my company and recommended that they no longer issue Commuter Check cards (see Warning). In any case, I won’t be using them again.