Yes, I suspect that because of the angle of the gutter you are probably not getting enough glue on the bulkhead side of the mating equation. I seem to recall dripping some glue on the bulkhead above the gutter and hitting it with accelerant just as the glue touched the gutter. I definitely recall doing A LOT of sanding in that groove to get the upper galley gutter to slip into the groove in the bulkhead
I wrestled with the bottom gutter for a long time, and still got it wrong. My mistake was jamming the lower gutter up too high on the side panels resulting in a slight, outward bow of those panels. I ended up cutting the fillet between the gutter and side panel and regluing it to get everything straight again.