I checked again to make sure, and the XML files I'm looking at are from the r349. As the base package is r327 with the r349 to be copied over it, I can't speak to any other releases. These files with r349 are from 5-6-2010 and GirlsAddon1.girlsx with CRC B99D2CE9 and Girls.girlsx with CRC 44E674E3. The problem may be sporadic, which as a technician myself, I know are the hardest types to troubleshoot. However, as someone who owns a car over 20-years old, I also know the frustration of taking a vehicle to the mechanic four or five times before he is able to see the problem himself.
With the pregnancy rates I did a real quick-like game with four pregnancies with the pregnancy set at 10 weeks and the maturity rate set at 5 weeks. The son and two of the girls were player induced with the last girl induced by customer. These were my results:
(Used Windows calendar to determine weeks)
03-04-09 Reimu - Pregnant
26-06-09 Reimu - Son sold into slavery (Did not show when born)(12weeks)
10-07-09 Hiiragi - Pregnant
20-09-09 Hiiragi - Birth Girl (10 weeks)
02-11-09 Hiiragi - Girl appears (16 weeks)
10-07-09 Helena - Pregnant
20-09-09 Helena - Birth Girl (10 weeks)
02-11-09 Helena - Girl appears (16 weeks)
24-07-09 Lum - Pregnant
04-10-09 Lum - Girl (10 weeks)
16-11-09 Lum - Girl appears (16 weeks)
As you can see, the son was 3 weeks early and the girls were all 1 week late. I wish I had the time to redo this with a greater sample for sons, but even if only once, this clearly shows that at least some of the time the sons are short circuiting their time routines. Without a greater son sample I can't tell if the result may be from the pregnancy, rather than maturity, routines. The majority of the time I do get birth messages for the sons (I think) so am not sure why I didn't on this one. I think I still have the game log and save game for this if those would be helpful.
Other things I noticed:
Practice skills don't work at all unless at least two girls are set.
Girls provisions are set to very poor when being sent to the dungeon from the management screen, but not returned to adequate or whatever when released from the dungeon.
Selling slaves or withdrawing money from the bank is included in profits for next day. This probably isn't really a bug, so much as game design. Still, from an accounting view, withdrawing 20K from the bank isn't the same as generating 20K income from an ongoing concern.