When I initialize a new blockchain, add a base account, and start a mining thread, Ether starts to accumulate into the base account. Generally I think of Ether transferred from one account to another account.
If there is no from account, where is the Ether coming from?
If the answer is that "it's reaping fees for mining transactions," then what are these "transactions"?
The second question vexes me because the miner seems really busy earning Ether mining transactions that no one is sending.
Blocks don't necessarily have to have transactions in them. You can actually have a completely valid block that doesn't mine a single transaction. This is relatively unusual, but it does happen.
These so-called "empty" blocks still give a reward through the "beneficiary" field of the block data. This is basically a magic transaction that 'mints' new ether and sends it to the beneficiary. Miners typically specify themselves as the beneficiary, but you could populate that field with any address.
Basically, your mining thread is finding valid blocks (and getting paid for it by the protocol), they just don't have any transactions in them!
