Indicators only spawn for the first 3 veins. All veins are loaded. I tried changing some values.
The file:
https://pastebin.com/BcVqfWbS

If there's not a problem here...

By the looks of it, I think your indicators are all spawning, it's just you're not specifying the metadata values correctly so it only looks like some veins are spawning indicators.

If you want an indicator to use metadata in the blocks tag, it needs to be an object:

"indicator": {
    "blocks": {
        "block": "minecraft:planks",
        "meta": 3
     },
}

See https://github.com/alcatrazEscapee/ore-veins#block-entries