Dear Clemens,
this is very strange, since the talairach.xfm is not by default overwritten in recon-all (unless you specified -clean-tal to recon-all).
When you rerun your recon-all after modifying talairach.xfm, your automatic talairach registration will be saved into talairach.auto.xfm, therefore talairach.auto.xfm and talairach.xfm will be different (without editing they will be identical).
See the excerpt of the recon-all -help:
Talairach (-<no>talairach)
This computes the affine transform from the orig volume to the MNI305 atlas using Avi Snyders 4dfp suite of image registration tools, through a FreeSurfer script called talairach_avi. Several of the downstream programs use talairach coordinates as seed points. You can/should check how good the talairach registration is using "tkregister2 --s subjid --fstal-avi". You must have an "fsaverage" subject in your SUBJECTS_DIR. tkregister2 allows you to compare the orig volume against the talairach volume resampled into the orig space. If you modify the registration, it will change the talairach.xfm file. Your edits will be *not* be overwritten unless you run recon-all specifying -clean-tal. Run "tkregister2 --help" for more information. Creates the files mri/transform/talairach.auto.xfm and talairach.xfm. The flag -tal-check will check the registration against known-good transforms. Adding the flag -use-mritotal after -talairach will use the MINC program mritotal (see Collins, et al., 1994) to perform the transform.
Can you check that your edited talairach.xfm is indeed modified to default after recon-all rerun? Do the talairach.xfm and talairach.auto.xfm differ?
Antonin