[bigstar]

Is the global skip list turned on?
Options > Filters > Skip list > "Enable skip list"

Is the per-site skip list turned on?
Site Manager > Options tab > "Use skip list"

The other factor is the "When to skip" setting in the filters > skip list, make sure you have it set to the desired value.

Automatic File Transfers
An automatic transfer occurs when FlashFXP en-queues nested files or folders within a folder that was manually queued.

Manual File Transfers
A manual transfer occurs when the user interactively queues or transfers an item.

Both
The skip list is applied to automatic and manual transfers.

I tested the per-site skip list and it worked as expected, I have "when to skip" set to both and attempted to manually transfer a folder named "old", in the status window it reported Skip [skiplist]: old

Update:
Make sure you add "old" and "_old"