I have encoded recipes in packagers resulting in 62 Recipe Packages that should appear in my ME network. On a subnetwork containing just Packagers and a terminal, all packages appear. Once connected to my crafting network, seemingly random subsets of these recipe packages appear and disappear every time I open the terminal.

When the recipe disappears, it also confuses the AE network and any Recipe Package items I have sitting in my ME network vanish until the packager recipe appears again.

The problem appears to occur regardless of whether I use AE cables, ME conduits, or adjacent-block pass-through to connect the packagers. Sometimes disconnecting and reconnecting the packagers from the network helps momentarily, but the recipes inevitably vanish again. I have billions of banked RF and several dense energy cells on my network, so the issue is not that packagers are unpowered. The pack by default disables channels in AE so it shouldn't be related to that either.

I have had no success in mitigating this problem and it is severely impacting my ability to progress in this modpack.

An illustration of the problem is available here: https://imgur.com/a/Rg7cAr3
(I would upload to the ticket directly but GitHub is giving me errors when I try to do so).

Modpack: Omnifactory 1.2.1
Applied Energistics version: rv6-stable-6
Packaged Auto version: 1.0.2.6 (also occurs in 1.0.2.8)

Omnifactory comes with PackagedAuto 1.0.2.6, but I updated to 1.0.2.8 to see if it would help any. The update has had no discernible effect on this problem.

Does this happen with interfaces?

I'm not sure I understand the question. If you mean do I also have AE patterns disappearing from interfaces, then no. All of my AE recipes in interfaces are working fine. It is only PackagedAuto recipes that have this issue.

Edit: Updating to Applied Energistics rv6-stable-7 also had no discernible effect. Still having the same problems as before.

Just to rule out the possibility of the problem being channels, I tried turning them back on. Naturally, I made sure that all connected devices had a channel.

Even with a setup as simple as:
Creative Energy Cell -> ME Controller -> Smart Cable -> Packagers with encoded recipes, one ME Terminal

...I continue to experience the issue: closing and reopening the terminal, random subsets of the recipe packages randomly disappear.

I have exhaustively fiddled with every variable I can think of and nothing seems to make any difference. I tried recreating my packager setup in a new creative test world with nothing else in it as well, and still have the same problem.

I have this issue as well, on Enigmatica 2: Expert. Pack version 1.72b, running PackagedAuto 1.12.2-1.0.2.9.

What would help to replicate this? I could provide a world backup, world size is 591.7MB so I'd have to throw it up on Mega or something.

Many, many moons later I'm back to update this issue and note that at least in my case, the problem was specifically being caused by using OpenJ9 JVM instead of Hotspot JVM. Below are two OpenJDK versions, switching to the hotspot JVM (first listed below) resolved the issue.

localhost ~ # /opt/openjdk-bin-8.252_p09/bin/java -version
openjdk version "1.8.0_252"
OpenJDK Runtime Environment (AdoptOpenJDK)(build 1.8.0_252-b09)
OpenJDK 64-Bit Server VM (AdoptOpenJDK)(build 25.252-b09, mixed mode)
localhost ~ # /opt/openjdk-openj9-8.242-b02/bin/java -version
openjdk version "1.8.0_242-internal"
OpenJDK Runtime Environment (build 1.8.0_242-internal-root_2019_12_05_20_35-b00)
Eclipse OpenJ9 VM (build master-154c39d2f, JRE 1.8.0 Linux amd64-64-Bit Compressed References 20191205_000000 (JIT enabled, AOT enabled)
OpenJ9   - 154c39d2f
OMR      - 7b2e5df4e
JCL      - 8514ba3391 based on jdk8u242-b02)

I'm not sure if this is even a bug that you want to pursue given that it's upstream in the OpenJDK implementation somewhere and AFAIK impacts all of AE2, not just PackagedAuto, but it may make sense to add a warning of some sort if the JVM is OpenJ9.