Comments are sometimes missing from the HTML-only view. For example, try finding comment #37499132 by user "bugnuts" in the following discussion in both the JS and HTML-only views:
Comments #37499256 by NoSig and #37500168 by pRock85 are also missing.
It appears that an entire contiguous block of comments has gone missing between pages 2 and 3 of the nested view. Some discussions are missing hundreds of comments. In general, a higher proportion of comments (sometimes hundreds) go missing in longer discussions. I have a suspicion that this may have to do with how long threads cross page boundaries. In some discussions with long threads (some with more than 100 comments in a single thread), subsequent pages would be identical or near identical. The software seems to try to start comment display on a new page at the root of the current thread. Maybe in some cases this leads to mis-counting how many new comments are being shown, and thus to gaps.
I discovered this in 2012 when analyzing older Slashdot discussions. I reported it but did not hear back. I suppose it is possible it has been fixed for newer discussions but not for old ones. Also, with the decline in commenting activity on Slashdot in recent years it should be less likely to occur.
To return to the original topic, I find the beta unusable because there is no way to display high-scoring comments with context, then expand out low-scoring comments to investigate surrounding threads. This destroys the value of Slashdot's amazing moderation system. Without it I can neither read nor moderate effectively. If it is done away with, I won't be coming back. I'm not a fan of the new look either, but unlike the integrity of the moderation system that is not critical.