The "line error" is a known bug existing in RC from he beginning. RC is emulating ANTIC and was created basing on awesome documentation prepared by Phaeron; during development it was tested also on his Altirra. However at the time Altirra had imperfect sprite emulation related to sprite repositioning (what is going to be drawn on the screen when you reposition a sprite to a location where "beam" is actually drawing it. Before RC, considering that there was nothing in the past needing exact behavior, no emulator had it properly implemented. After Phaeron fixed Altirra and wrote good description of what Atari is exactly doing in such situation, I planned to fix the RC too. However meanwhile Phaeron implemented to RC multi-threading and huge number of optimizations. Fixing the problem in such optimized code is not easy, as I had no time to understand exactly how the optimizations he implemented work. Phaeron can be probably the best person to fix the bug now, however none of us touched the RC code for a few years now. Other fix "by hiding the problem under carpet" could be by "rejecting solutions" during the emulation phase. Program there could check if sprite is repositioned to a position where it would trigger the bug. However also this would require better understanding of the emulation caching Phaeron did. I unfortunately work on some out-of-Atari projects and don't have time to get back to this.
As RC is random by nature if you run a few conversions of the same picture in parallel, most probably some of them won't have bugs. Also as you found out - the longer RC works, the bigger chance of the bug there is. RC works by iteratively finding better positioning of the sprites and changes of color registers. At one point to progress it needs to "reuse" the sprites. If it finds out that the best reuse is by placing it to overlapping area of previous sprite position, we have a bug.