vinnie97, it sounds to me that your "audio drop out" on "Sunshine" had more to do with the entire player choking (i.e. the video came to a crawl as well) and not really in the same family as the other audio drop outs we've experienced.
Last night I discovered that Ocean's Eleven, another one of the films on my list of Warner Bros movies that cause the player to switch to 60hz mode, also had audio drop outs. So far my theory that if a disc has one issue (60hz only) it'll have the other as well (audio drop outs at the chapter change) holds true. It's also possible that all of these discs have the same kind of audio track (Dolby Digital), which is something I should look in to.
It seems to me at this time that Blu-Ray discs aren't susceptible to only displaying at 60hz mode or the chapter-marker-induced audio drop outs (except in situations where the whole house comes crashing down, i.e. Sunshine). Rather, just SD DVDs and some HD DVDs have these issues. This would make sense, considering HD DVD is just a souped up version of standard DVD, and manufactured in the same fashion. Since the BD-UP5000 will only display SD DVDs at 60hz, perhaps those Warner Bros discs which also cause the player to switch to 60hz are closer in relation to SD DVD than those which do not? Regardless, it's highly likely that all of the Warner Bros films that have audio drop outs and display only at 60hz were authored for Warner by the same company, with the same software.