Hi Phil,
I've got one theory...
The main difference for imports between PHPmyAdmin and Sequel Pro is that PHPMyAdmin is (typically) running on the same server or network as the MySQL Server, whereas Sequel Pro can run from a different location. This means that ping/lag will typically be higher for Sequel Pro.
Depending where you got the SQL file from, it may use lots and lots of small queries. Each of these is run individually, which magnifies the effects of ping; in a high-bandwidth high-ping situation, this means that running the import from PHPMyAdmin will be faster.
Many programs attempt to batch queries in exports for that reason. For example, when you generate a SQL export with Sequel Pro, it tries to combine the data into queries of around 250k in size, to minimise the effects of network ping on a subsequent re-import.
If you look at the SQL file and the network conditions, does that sound like it might explain it?
Rowan
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