Is their evidence of RNA secondary structure causing a stall in translation within a eukaryotic cell?
Can a hairpin (stem loop) within a transcript stall a eukaryotic ribosome?
It seems that could happen. C9orf72 translation is one of the examples. In this gene, GGGGCC repeats exist in 5' UTR of the mRNA (upstream of the first ATG). The repeats expand in subsets of neurodegenerative disorder such as ALS. The repeats can form a stem loop structure and stem loops of expanded repeats are more stable.
mRNAs having expanded repeats seems producing poly-GlyAla, poly-GlyPro, and poly-GlyArg peptides which codons are GGG-GCC, GGG-CCG, and GGC-CGG from different frames from GGGCC repeat.
This means the translation starts somewhere in or upstream of the repeat without ATG. To explain this, there is speculation that ribosomes stall because of the tight structure of the stem loop by expanded GGGGCC repeats, mistakenly take tRNAs and start translation. It is called "Repeat-associated non-ATG translation".
You might want to refer to: Repeat-associated non-AUG translation and its impact in neurodegenerative disease. https://sites.tufts.edu/als/the-answer/c9orf72/ RAN translation and frameshifting as translational challenges at simple repeats of human neurodegenerative disorders