I am using the latest version of this mod, also it happens inside a Giant (diamond) compact machine. I have better barrels from JABBA inside, Tesseract from thermal expansion, conduits from Ender IO and liquids such as water and lava to create a cobble gen using transfer node (item) from Extra Utilities. when I break a blocks (any) inside the Compact Machine, it disappears into the void. Any idea how to fix this? maybe I am using too many entities with my cobble gen? (I have 35 transfer node with respectively 64 world interaction upgrade in them generating cobblestones). Any help is appreciated.

Two options:
a) Upgrade the CM with a Nether Star so it retains its content when being broken.
b) Set the maxDroppedStacks option in the config file to -1 to always drop all stacks when breaking a CM.

blocks broken INSIDE the compact machines disappear into the void, I did not break the compact machine and fyi it is equiped with a nether star and the maxDroppedStacks is already set to -1