Summary
You have not encountered an error in your copy of the blockchain.
As you have observed, there are no transactions in the blocks 1 to 46,146. This was the first 7.5 days of the Ethereum blockchain. Part (or all) of this period is the thawing period, where security through mining is built-up but no transactions are allowed (Thanks @tayvano).
The Details
Here is a script to check the number of transactions between a starting block number and an ending block number:
function checkTransactionCount(startBlockNumber, endBlockNumber) {
console.log("Searching for non-zero transaction counts between blocks " + startBlockNumber + " and " + endBlockNumber);
for (var i = startBlockNumber; i <= endBlockNumber; i++) {
var block = eth.getBlock(i);
if (block != null) {
if (block.transactions != null && block.transactions.length != 0) {
console.log("Block #" + i + " has " + block.transactions.length + " transactions")
}
}
}
}
Running the scripts for blocks 1 to 46146 shows the following results - there are no transactions!:
> checkTransactionCount(1, 46146)
Searching for non-zero transaction counts between blocks 1 and 46146
undefined
Let's check that the script is working as expected:
> eth.blockNumber
1382234
> checkTransactionCount(1382224, 1382234)
Searching for non-zero transaction counts between blocks 1382224 and 1382234
Block #1382224 has 4 transactions
Block #1382225 has 2 transactions
Block #1382226 has 4 transactions
Block #1382227 has 6 transactions
Block #1382228 has 17 transactions
Block #1382231 has 2 transactions
Block #1382234 has 1 transactions
undefined
There are some transaction included in 46147 to 46200:
> checkTransactionCount(46147, 46200)
Searching for non-zero transaction counts between blocks 46147 and 46200
Block #46147 has 1 transactions
Block #46169 has 1 transactions
Block #46170 has 1 transactions
Block #46194 has 1 transactions
undefined
Let's check the time between blocks 1 and 46146:
> eth.getBlock(1)
...
timestamp: 1438269988,
...
> eth.getBlock(46146)
...
timestamp: 1438918224,
...
So there are 648,236 seconds between the block range 1 to 46146, which is 10,803 minutes, or 180 hours, or 7.5 days.
This must have been the initial burn in period. Edit 23/04/2016 - Part (or all) of this period is the thawing period to build up security through mining, but no transactions allowed (Thanks @tayvano).