Hmm, come to think of it, I've also noticed that sometimes a dialogue entry is not where I thought I put it. I wonder if Error Checking also moves dialogue entries around. Sounds like I should follow Kir's advice and NEVER SAVE after Error Checking. I'd better go eyeball all my dialogue to make sure nothing else is screwed up.
The moving of dialog entries... are some new entries being moved to the bottom of the list in a given topic? While this may be happening as a result of using TESAME to clean your mod it is not really its fault. Any third-party utility will have this effect. Even toggling the ignore flag of the mod's details before loading in the construction set will break the dialog pointers around (and particularly below) the
new dialog entry deleted. However, if you load the mod, open the dialog window and DELETE the undesired entry, the next time you load the mod in the editor (or in the game for that matter) your remaining dialog will be properly ordered.
I first http://forums.elricm.com/emma/viewtopic.php?t=516&start=16 over at Emma's Forum. Kateri explanation while not particularly detailed helped me understand what must be happening. melian's tests confirmed this phenomenon.
I offered a more detailed explanation in my epic "Conventional Wisdom on Cleaning Dialog" thread. The last entry was about three years ago so it has been subsequently pruned from the construction set forum. However Yacoby was kind enough to preserve that thread in his http://www.yacoby.net/es/forum/11/6816271177042920.html. The first part of that thread discusses the merits of cleaning the insertion points around new dialog. The relevant posts begin with mine on 9 May, 2007 (after the block of LGNPC dialog conventions).
What is not included in that particular post (but followed up on 11 May, 2007) is what I mentioned earlier (and have confirmed through testing). You can easily and safely remove unwanted new dialog entries by 'deleting' it while in the dialog window. The entry is flagged 'DELETED' and will be removed after the mod is saved and subsequently loaded. The reason this works is the editor is able to reassign the dialog pointers to ignore the deleted entry thus giving a continuous path of next and previous entry pointers. When this is done outside the construction set (or by toggling ignore in the mods details just before loading it) the entry is removed, but the line above it has a next pointer (NNAM) with no object and the line below it has a previous pointer (PNAM) with no object. These get tied off to the nearest official entry and the block of new dialog below the deleted entry gets moved to the bottom since nothing is pointing to its top entry.
These concerns about deleting new dialog entries are only an issue for dialog added to existing topics. If you delete an entry from a topic you have created there is no scrambling of the order of the remaining entries from what I have observed. However if two mods add the same new topic and one (or both) deletes an entry using a third-party utility such as TESAME, there could be some strangeness when they are loaded with the game. I am not certain it would be an issue, and it is such a remote possibility that I do not worry about it.