Aggressive indexing is the heaviest in terms of resources. It takes a long time especially against a large library since it has to scan each file in full. The only benefit it may provides is that it'll attempt and do a better job of estimating the total time of variable bit-rate MP3s. Otherwise it is unnecessary. The rest of the indexing options do only the header and a few frames into the file.
Do you have the same problem with more relaxed indexing?
I just tried both fast and normal indexing with the same results.
I first noticed the problem after I updated the ID3 of some of my mp3s using a util called MediaRage. This is the same util I have used on most of my mp3s to add album art. I decided I wasn't using RSync or uPNP, so I turned them off and rebooted my box. After reboot and reindexing, the files I had updated were no longer showing ID3 info. These same files were updated using MediaRage before I had NL-M2 and showed all ID3 info when first loaded into my MEDIA folder. I loaded them into my iTunes library via AFP and the ID3 info showed normally. I then noticed that there were many more files that had valid ID3 info that were not showing the ID3. Album art shows in all of them. I can also load the files into WMP, Winamp and VLC via AFP and ID3 is read. It seems to be affecting the last 1/3 or so of the files that are indexed. I tried deleting the ID3 and rewriting, reloading the files from backup and reindexing several times. Even tried booting my M2 v1.00 copy and reindexing to check if it was a bug in 1.01. Nothing has worked.
I'm picking up a couple of 512M sticks this weekend. Perhaps that will make a difference?