Can a $100 bill be fake only by marker test?

[John]

So my sister-in-law paid me for a previous persnal loan of $1400 cash. I was somewhat glad for the payment because I could use it. I take it to the bank to deposit it. The teller fans out $1400 then runs a testing marker over all of them. Then she takes a closer look at a 100 bill, pulls it out, marks it again. She flips it over and marks it again and again everywhere. All this time not saying a word. At this point I was concerned. Apparently the ink was turning brown on the $100 note (it would be yellow if ok). So she checks the watermark, its there. She checks the color changing ink, its there. She checks for the little strip, its there. She checks for the red/blue fibers in the bill, its there. Everything was there except the marker ink wouldnt pass. Even the manager and other tellers was amazed about the quality of this "counterfeit" bill. Everyone in the bank wanted to see the quality of this fake bill. Their words were somewhere along the lines: "This is the best counterfeit I've seen in my life." Long story short, I was told there's nothing I can do, they wont return the bill, and I'm out $100. They deposited $1300 and kept the "fake" $100. So, was I screwed over or do you think the $100 was truly a counterfeit?