Hi Jake,
The reason the LineOrder number reverts back is because Quickbooks will not allow you to rearrange items that are already on the estimate. You can only set the LineOrder on a brand new item. The only work around for changing the LineOrder of existing items it to recreate the item, set the LineOrder column to the correct number, and then delete the duplicate.
If you like, you can always create a new field and sort the grid differently as Andy suggested, but you would have to customize something similar on the reports as well.
Jason