In Omnivore there is a setting called: Maximum stock quantity in Trade Me. You can find it in Omnivore under 'Settings - Trade Me - General' under the 'Your Products Section'.
Omnivore will set the inventory of your products to the number that is in this field.
By default it is set to 1 so that if you have small changes in inventory, Omnivore won't need to update your products on Trade Me as frequently as this can slow the updating of products down.
You can change this setting to another number (as per the dropdown) then click 'Save'. Go to the Dashboard and click 'Upload to Trade Me' to update your products.
Note that if the maximum quantity is say 5 but you only have 2 in stock, Trade Runner will respect the lower quantity and send a stock of 2 to Trade Me.