Hi Frank,
I'm not sure if there was a specific rule/law to declare Jews stateless in Czechoslovakia based on a parent's emigration to the US. However, I'll tell you want happened with my maternal grandparents, which may provide a clue.
My grandfather left Czechoslovakia in 1922 to establish himself in America. He obtained his US citizenship in December 1927, returned to Czechoslovakia and married my grandmother in Rosvigovo, a suburb of Munkacs, in November 1928. My grandparents planned to come to the US after the wedding, but the Czech government would not give my grandmother a passport. Their reasoning was that since she married a US citizen, she was no longer a Czech citizen. To the best of my knowledge this had nothing to do with her being Jewish. Anyway, they found a lawyer/notary in Prague who provided my grandmother with a document she could use in lieu of a passport (I have that document). They arrived in New York in March 1929.
Based on what happened to my grandmother, I'm wondering if, during your uncle's attempts to get a passport, the Czech government determined that his father was now a US citizen, which in their eyes, and possibly a rule/law, voided your uncle's Czech citizenship (now being the son of a US citizen). Just a thought.
Regards,
Mark Resnicoff