After some more precise testing which led the discover a cause of dropped stack becoming invisible, possibly timer by the oldest item. I have revised steps to reproduce below. I recommend that you use stopwatch to track individual items' despawn timer in the stack.
Steps to reproduce
1) Pick any item a stack of 64 and place in your hotbar.
2) Start stopwatch as soon after you throw 1 item down on the ground. Throw other item at 1 minute of stopwatch and wait until 5 minute of stopwatch. Be sure these items stack up together.
3) Wait for the stack becomes invisible. Start throwing items down individually, you will see them disappearing while stacking up into the invisible stack.
4) Go into the space where items were disappearing. Watch the item you are holding and in hotbar, picking up the invisible stack.
Dropped stack becomes invisible after the initial despawn timer by the oldest item. It is as if the game uses 2 timers; from the oldest item that cause stack invisible when it has reached 5 minute despawn timer, and the most recent item resetting stack's despawn timer normally. Continued being invisible until the timer has been reached and despawned.
Items should not disappear while stacking up into the visible stack. Dropped stack should have timer resetting to 5 minute by the recent item and is visibly on the ground. (1 timer per stack?)
Affected WITH and WITHOUT chunk border setups.