Is bouncing better? I also have to try the virtual part of Samp. I haven't figured that out yet.
Here is how I would track out a project with Samplitude to create 16-bit files which you could flac. You don't need to adjust your original files. And it's possible to do this without bouncing.
First create a virtual project. Then load your audio files into the project using File->Load Audio File . Let's assume that you have multiple 24-bit files and they have seamless breaks. When you load each file it will create an object.
Set "snap on". It's the button with the little magnet. Drag each object to the left and it will jump into position to align perfectly with the object on the left. To move objects around you need to be in "universal mode" or "object and curve mode" and click on the lower half of the object to select it. Then drag it with the mouse.
Now once all your audio is loaded, the next thing you want to do is to split each song into it's own object. This makes it easy to set track markers later. At the beginning of each song, press "t" on the keyboard and this will split the current object at the current cursor position.
Once all objects are split, then from the CD/DVD menu, "Set track indices on object edges". Next, position the cursor at the end and select "Set CD end". (If you have more than 80 minutes of audio you will need to deal with each 74 or 80 minute segment separately. A CD can be any size from 0 to 80 minutes total.)
Then save the project. This is important because the CD audio code reads the project file for information. Now you are ready to burn the CD. Notice, that at this point, no 16-bit files have been created yet and no bounces were required. All changes were made in the VIP and your audio is in it's original format. The VIP determines what happens.
Finally, mark the range from track marker 1 through CD end. Then from the CD menu select "Make CD" and follow the dialog. There are options for dithering and CD burn speed.
Once your CD is created, you can import them into a new project using File->Load Audio CD Tracks or use ExactAudioCopy (which is my favorite for that). This I think is the fastest way to do this. You could also bounce each object to a 16-bit file, but that would take a bit more time.
There are different ways of doing things in the software. I'm not saying this is the only way or the correct way. It's just a quick way (having used the software for a good while I would recommend it).
Each 80 minute or less segment of audio can be dealt with in this manner. All you have to do to make a CD for each part is set your CD markers, set your end CD marker, save the project, mark the range and then and make CD.
Gordon