I’ve spoken to the developers of the Woocommerce Bundle plugin and this is their feedback:
To further explain the issue you encountered, up until v5 Product Bundles was applying discounts or price modifications in general in the cart as early as possible. This was acceptable in most cases. However, we’ve received a couple of reports about other plugins that modified product prices after Product Bundles. This could result in bundled product prices being completely overridden. The most common case was when Priced Individually was disabled. In this scenario, Product Bundles was setting bundled items prices to 0. Then, some other plugin modified the product prices and reset bundled items prices back to their original value.
From v6 onwards, Product Bundles is applying discounts as late as possible. This should resolve most of these issues, but at the same time you may see another issue when using our own bundled item Discount feature in combination with some dynamic pricing plugins:
Let’s say a plugin applies a 50% discount to all customers who shop on a Monday. Now imagine there’s a product that normally costs $100, which is also included in a Bundle with a 20% discount:
* With v5, the PB discount would be applied first, so $100 – $20 = $80, and then the third party discount plugin would further discount that $80 to $40.
* With v6, the third party discount plugin will first discount the $100 to $50. So far so good. Then, PB will apply its discount over the regular price by default, so it will replace that $50 with $80.
In short, in order to maximize compatibility we are currently offering two methods for calculating prices of Product Bundles in the cart — however, there are still some plugins that will not play nice with either of these methods.
Perhaps this will help in resolving the issue on your side?
Thanks