When I press the vein mining key and try to vein mine a oak tree with a iron axe I only mine the one block that I was hitting.
Mining ores works fine.

Details:
forge-32.0.75
excavation-1.5

excavation-common.toml:

[client]
	#Disable the keybind and activate excavation by crouching.
	crouch = false

[server]
	#All blocks are placed in the player's inventory unless it is full (False [Will cause extra lag])
	vacuum = false
	#Maximum blocks to break with one excavation (Integer)
	#Range: > 1
	max = 64
	#Multiply the default Minecraft block exhaustion by this much (Double)
	#Range: 0.0 ~ 1.7976931348623157E308
	exhaustion = 1.0
	#Does the player need to mine with a valid tool?
	tool = true

excavation-groups.json:

[["minecraft:oak_log"]]

excavation-server.toml

["General Category"]
	#All blocks are spawned under the player (0 false, 1 true)
	#Range: 0 ~ 1
	vacuum = 0
	#Maximum blocks to break with one excavation (Integer)
	#Range: > 1
	max = 64
	#Multiply the default Minecraft block exhaustion by this much (Double)
	#Range: 0.0 ~ 1.7976931348623157E308
	exhaustion = 1.0
	#Does the player need to mine with a valid tool? (0 false, 1 true)
	#Range: 0 ~ 1
	tool = 1

The server config still exists? It shouldnt. Did you use the mod before 1.5? Also looks lile you have tool mode on, were you using an axe to mine the tree? This version of the mod was developed on forge 32.0.106, maybe the outdated version could be an issue? Maybe having vacuum mode off could be causing issues? It creates a bunch of lag and I haven't tried making sure its working since i added vacuum mode into the mod.

I have used the mod before 1.5. As you have stated, that the server config shouldn't exists any more I deleted it.
I also updated to forge-32.0.108 which did not fix the issue.

After disabling tool mode I was able to vein mine a tree. With tool mode enabled I can't vein mine a tree. And yes I am using an axe. To be precise an iron axe.
I also saw that vein mining nether quartz with an iron pickaxe was not possible while the tool mode was enabled.

Conclusion:
Tool mode is broken

Thank you! This helps narrow down the issue, I shall look into this as soon as possible