Ok, Mr_Spuck found this one first, and he and i experemented with it for a bit, what basically happens is that the cargo being sorted into alphabetical order doesn't change a listing somewhere else.
That listing (i'll call it LIST 1) remains sorted by what order you aquired the cargo in. List 1 is used by the cargo jettison menu, and the sell menu in station.
The alphabetical list in the cargo tab (LIST 2) appears to be used only in the cargo tab. When you click on an item in list 2, it highlights, and moves, the wrong cargo. It highlights the cargo in list 2 that has the same position as the cargo you clicked occupies in list 1. for example, Purchase the following list1 of cargo.. in this order from a station.

In your jettison menu list1 looks like this, the order you buy it in.
Ferric Ore
Purified Water
Synthetic Hydrocarbons
Ishik Ore
Aquean Ore
Steel
NanoFeed
Carbonic Ore
Volitile Chemicals.

When the list is sorted into list 2 in a station within the cargo tab it will look like this

Aquean Ore
Carbonic Ore
Ferric Ore
Ishik Ore
NanoFeed
Purified Water
Steel
Synthetic Hydrocarbons
Volitile Chemicals.

when you click on Ferric ore in list 2, it will highlight aquean ore, because aquean is the cargo that corresponds to where ferric is in list1. By the same token to get ferric ore to highlight in list 2, you have to click on synthetic hydrocarbons. since that was the 3rd cargo you purchased, and ferric is the 3rd cargo alphebeitcally, ferric will highlight.

Noticed the same bug this morning.

Broma-ba Slick

doh. apparently i didn't test it well enough.

[edit]
Ok, it's fixed for the next update.

Thanks Ray for fixing so quickly. (And for the alphabetical lists).