Are you using partitioned tables or indexes?
This is probably something we're not preserving correctly in Sequel Pro at the moment - if there's any chance you could send me your CREATE TABLE syntaxes directly, we can probably get that sorted for the next version...
Thanks,
Rowan
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Thanks for the extra info.
There is something odd here - when you're changing the structure, all that gets sent is an ALTER TABLE command with only the details needed to change, for example a row edit. So the table setup shouldn't matter. That and the key file errors makes me suspect that when the tables were created, phpMyAdmin specified an incorrect storage directory.
This can be seen in the CREATE TABLE query you selected as:
... DATA DIRECTORY='./wwtweb_webstreet/' INDEX DIRECTORY='./wwtweb_webstreet/';
Are those paths correct and writable?
On the other hand, you say you can add records to any table, so I'm not entirely sure that that's the problem. But I don't think it's default behaviour for phpMyAdmin to specify directories, and the incorrect key file error is very suspicious (that's an error thrown by mysql).
--Rowan