Retirement accounts 401(k) with negative cash balances

It sounds like Quicken and the QFX import are functioning correctly. When the BUY transaction occurs in the 401K account, it uses up some cash in the account. Since you have no transactions showing that cash coming into the account, that's why it builds up a negative cash balance. To fix this, you need transactions that show the cash coming into the 401K account, which will be "used" by the BUYs and result in an ongoing zero cash balance. So in this case, you should do two things:

1. In your paycheck transaction in your checking account, you should presently have a split line for the 401K deduction. In that split line, instead of whatever Category you have now, you should change it to "Transfer" and then in the Transfer column, enter the 401K account. This will move that cash into the 401K and partially offset the BUYs. (Alternatively, you can enter "Transfer:[401k-account-name]" in the Category column and avoid using the Transfer column.)
2. Now we need to account for the employer contribution. This input to the 401K is outside of your paycheck, so you need to create a transaction each period in the 401K showing the employer contribution. It should be a transaction of type Payment/Deposit, a positive amount in the Amount column and a category such as "Employer 401K Match" or whatever you want to call it. You can make this a scheduled transaction each pay period so you don't have to enter it manually each time.

As an alternative to #2, you can build the employer match into your paycheck transactions so that you don't need a separate scheduled transaction in the 401K account. In the checking account, this paycheck transaction would look something like this:

Your actual paycheck will of course have many more deductions. I showed only Federal Tax in this example. Note that the “income” for the employer match is offset by the transfer of the same amount to the 401K account so that it doesn't affect paycheck's bottom line.

Over in the 401K account, it will look like this:

Note that the total cash balance will remain at zero after each pay period.

It would be great if the QFX imports from Empower included the cash deposits into the 401K account, but apparently they don't and there's probably nothing you can do about that. So one of the above solutions will be the way to handle it.