problems bouncing interleaved stereo to split

I think this may clarify things:

854 Chapter 38
*Working With Split Channel Audio File Formats*
Logic Pro treats audio files with a name that ends in .L or .R as stereo files. This applies
to all file management functions, such as Rename, Create, or Revert to Backup. The
following list outlines how split stereo files are handled in Logic Pro:
 When you select an independent mono file (one side of a split stereo file “pair”) in
the file selector box, both channels are imported. Split stereo regions are indicated
by the stereo symbol: two adjoining circles.
 You can see both files in the Audio Bin. They have the same name—apart from the
channel suffix (L and R). If you rename one channel of a split stereo audio file, the
other channel file is automatically renamed as well. This also applies when renaming
regions associated with the files.
 File edits performed in the Sample Editor apply equally to both files.
 If you use the Add Region command to create a new region, Logic Pro does this for
both audio files.
 Any alteration made to either region is automatically mirrored by the other. This
applies to region start point, end point, and anchor position changes.
 If the region of either file is moved into (or within) the Arrange area, the other region
is also moved.

*Disconnecting Split Stereo Files*
Both sides of a split stereo file are normally edited together, as discussed above. On
occasion, however, you may need to edit one side individually.
To disconnect a split stereo file:
1 Select (either side of) the split stereo file in the Audio Bin.
2 Choose Edit > Disconnect Selected Split Stereo File.
You can now edit both sides of the recording as individual mono files. This function will
only disconnect one split stereo file at a time.
Important: If you want to reconnect the files, don’t define any new regions!
To reconnect all split stereo files in your project:
m Choose Edit > Reconnect All Split Stereo Files in the Audio Bin.
Logic Pro reconnects all disconnected stereo files in the project. Only files that were
previously part of a split stereo “pair” are reconnected.
Converting Split Stereo Files to Interleaved Stereo
You can convert two (split stereo) audio files into an interleaved stereo file—in the SDII,
AIFF, or WAV format. This is useful if you want to use a split stereo file in another
application, such as the WaveBurner CD mastering software, which only supports
interleaved files.
To convert split stereo files into interleaved stereo files:
1 Select the audio files in the Audio Bin.
2 Choose Audio File > Copy/Convert File(s).
3 Choose Split to Interleaved in the Stereo Conversion menu.
4 Type in the desired file name, browse to a folder location, then click Save.
Note: This only works for split stereo files. You can’t use these commands to combine
two mono files into a stereo file.