On Availability matrix tab, the system lets the user manually change the price for packages on specific dates or long term intervals, even for packages that are derived from your base rate.
After doing this kind of change, the calculation trigger (that could be an increase/decrease of amount or percentage) is broken and this is why the prices won't reflect the correct amount you were expecting anymore.
This is set to offer more flexibility in managing your package prices, but we are definitively going to work on a way to make it clearer in the system.
For now, we recommend you avoid customizing package prices from within availability matrix page. This should be done from the Rate Plans & Packages section only.
Any changes in your base rate can be done normally.