Most people I hear that have issues with not saving is importing lists from people or using custom coded lists. Me and my 4 friends who all bot all season have never had items lost or deleted when it should have saved, but they all do the same as me manually set every single item in the list 1 by 1 in trinity.
It's very ironic that you say this because it's what my conclusion is at this point.
For example, Crazy's ItemLists...
I run multiple bots, so when I found his ItemList post, I decided that I wanted to add some more items to my list for other builds.
I loaded his list on BOT 1,
Brought up my current ItemList on BOT 2,
I scrolled through both lists and added items from his list on BOT 1 that were missing from my list on BOT 2.
I then exported the list from BOT 2 and used it on all of my bots.
Everything seemed to work fine.
A couple of weeks later there seemed to be an outcry for an all-in-one list from Crazy, and I was starting to gear additional characters and needed to use new lists.
I imported one of Crazy's lists, then used the BOT1/BOT2 approach from earlier to add the Crusader, Barbarian and Monk items.
I posted this exported list from this and received feedback that an error was received when using it.
A new version of DB had dropped. After installing, I tried to import the list I had posted. I received a memory error. No matter what I did, I couldn't import it.
Instead, I grabbed the Trinity.xml from my old folder, and placed it into my new install. Brought up my ItemList and hit export.
I compared this exported list to the one I posted using a file comparison tool. They were exactly the same.
I tried to import it to another bot, but I got a memory error still.
After that, I used the Bot1 and Bot 2 method described earlier to create a new custom list that would work for all of my characters, using Crazy's List as a reference.
This new list I was able to export and import without issue.
I do not have any trashing issues with this list I made on my own.
I don't think it's directly any fault of Crazy, but perhaps something happened since some ItemLists were posted that caused them to toss unforeseen errors?