Thai Visa Dilemmas

We arrived at the Malaysian border around 8AM, departed the train taking our luggage with us.  We were close to the end of the queue, but it seemed to go steadily along.  When it was my turn to be processed through Thai customs, he looked at my passport and told me I owe 2000 baht ($40), because I overstayed my visit by 4 days.  I showed him my visa, which allows me 90 days, but then discovered it wasn't stamped at the airport when we arrived, so I received a 30 day stay. The whole process was exceedingly slow, and we needed to board the train to continue our journey into Malaysia.  He took multiple pictures of me, my passport, visa, departure slip, and rechecked Hoss's documentation.  I truly thought he was going to make me go back to the airport to get the stamp.  Finally, finally, finally...he gave me my much desired stamp, and away we went to Malaysian customs, which took less then 20 seconds.  We climbed aboard the train, which they very kindly held for us, and a couple others who had the same issue as mine.  A young British couple had more trouble than me, because the train left without them!!  I now hear that this is a common mistake, even though upon entry at the airport, we were in the visa line, and I told the immigration officer I had a visa.  Lesson learned...always check your documentation for accuracy!