"The values are correct in the transaction (in the 'Inv Amt' column), but don't show up in the 'Cash Amount' column and therefore don't impact the cash balance.
"The help from Quicken says this can be caused by having placeholders for the security, but there are no placeholders for these securities any more (I resolved them by adding all the historical data manually)."
It's a common mistake: (at least) in older versions of Quicken "resolving" placeholders does NOT delete those placeholders, 'resolving' a placeholder simply hides that placeholder.
[In versions of Quicken from Q2010 and later, but not in Q2004 or earlier (sorry I can't be more precise), you can see hidden investment transactions by going to Edit > Preferences > Investment transactions and putting a checkmark in "Show hidden transactions".]As long as a placeholder remains in an account, it will affect other transactions for the same security with a date on, or before, the placeholder date. The placeholder will affect other transactions by preventing those other transactions from altering the cash balance of the account. That is one of the purposes of placeholders: to allow the user to enter transactions for a given security that do not alter the cash balance of the account.
If you do not want a placeholder to be able to affect other transactions in the account, you must insure that the placeholder transaction no longer exists in the account.
["Placeholder" is another name for "Adjust Share Balance". A placeholder has an Action value of 'Entry'.]In a subsequent post in the same discussion, the original poster says, "It appears that the problem securities are being purchased as 'BoughtX' and not 'Bought'. I have no idea why. This was confirmed when I exported the QIF file and looked at it - for every manually-entered Buy transaction there was a matching 'XIn' transaction for the cash. Ditto for the manually-added Dividend and Sold transactions."
Normal Quicken behavior for transactions affected by a placeholder. The XIn supplies the cash needed by the BoughtX transaction (the XIn is a transfer "back into the same account"). That allows the Buy transaction not to affect the cash balance of the account - and the cash for the Buy comes from ... nowhere (like a Quicken created account opening balance transaction).
"All of the imported transactions are fine - this is only a problem with manually-added transactions."
It doesn't matter how the transactions get into the account (manual entry or downloaded); what matters is whether the transaction is for a security named in a placeholder, and whether the transaction has a date on, or before, the date of the placeholder, and whether the transaction would normally affect the cash balance of the account (reinvest dividend transaction, for example, could pass the other tests, but it does not normally affect the account's cash balance.
"When I open the 'Buy-Shares Bought' transaction dialog, I do see the section for cash handling ('from this account's cash balance' or 'From' another account). However, when I then select the security I want to purchase, this cash handling section disappears."
Exactly the behavior to be expected for a transaction being entered that is affected by a placeholder.
As noted above: the original poster has not "deleted" any placeholders, he has just hidden them. Hidden placeholders still affect transactions entered after the placeholder has been "resolved".
Finally (after I composed the above), the original poster added another post - now saying he's using the Subscription version of Quicken. Anyone having one of the newer versions of Quicken, can simply ignore any Q2000 specific comments above - but most of the above comments are applicable to all versions.
The solution, in a nutshell: delete the placeholders, and any related transactions such as "Balancing cash adjustment[s]".
[For users with versions that do not allow displaying hidden investment transactions, I believe the user can temporarily (one-by-one): modify the transactions that "resolved" the placeholder (by altering the number of shares in the transaction), delete the now visible placeholders, then modify the resolving transactions back to their original number of shares.]