Check your settings in View, Current View for the newsgroup.  You might
be hiding/filtering some messages.

If you've set to Group Messages by Conversation (which you'll want to
have replies groups together), you'll probably also want Tools, Options,
Read, Automatically Expand Grouped Messages or else you'll need to click
the + in front of a message to see replies.

Also look at Tools, Message Rules, Block Senders list to see if you are
blocking any senders for newsgroups.

As for doing delete/reset clean up any potential problems, you want to
do a RESET on the problem newsgroups at Tools, Options, Maintenance,
Clean Up Now.  A Delete won't fix problems with what has or hasn't been
downloaded.  And if you did a Reset of the newsgroup list at Tools,
Newsgroups, that won't fix newsgroup problems.  That redownloads the
list of newsgroups on the server, not the messages in the newsgroups.

One additional thing, if people are replying via different news servers,
that can account for missing messages.  Messages often get lost between
news servers.  This can even be a problem for people posting via the web
interface verses the NNTP news server.