Managers are available at two different stores.  
When doing the check business command I get the following message: No manager available when I have the following conditions:

1: No business related hacks
2: Your Check in with Shops Faster
3: Your check in with shops faster plus Pescadero's Missing Manager Fix

I have manager contact when checking in if I have Pescadero's Missing Manager fix installed however regardless of the other business mods (mostly yours).

These are the results when I have the business owner check into businesses from home.  Heck the way Pets messed everything else up, wouldn't surprise me if they messed this function up big time as well.

Tested with same lots and owner without saving the game each time during testing so I could repeat identical conditions for each set of mods/hacks.

Doc

Squinge I just tested the CheckInWithShopsFaster&NoTryingToCall package and found it conflicts with Pescadero's Missing Manager Fix package.  Without his package still was unable to contact managers. Combined with this package still unable to contact managers for checkin.  Just in case it will help figure it out here is what the hack conflict report said about them:

*** POSSIBLE CONFLICT DETECTED ***
File Type: BHAV
Procedure Name: Lots - Check In
Group ID: 0x7F2272AA
Instance ID: 0x0000100B
Packages Containing This Procedure:
\downloads\a hacks\matv\missingmanagerfix\missingmanagerfix.package
\downloads\a hacks\squinge\CheckInWithShopsFaster&NoTryingToCall\OFB_NoTryingToCall.package
 
*** POSSIBLE CONFLICT DETECTED ***
File Type: BHAV
Procedure Name: Lots - Check In All
Group ID: 0x7F2272AA
Instance ID: 0x0000100D
Packages Containing This Procedure:
\downloads\a hacks\matv\missingmanagerfix\missingmanagerfix.package
\downloads\a hacks\squinge\CheckInWithShopsFaster&NoTryingToCall\OFB_NoTryingToCall.package

I don't know if this will have much bearing on the mod, but I have noticed that after OFB, my controlled sims were only able to sleep on lots which they owned regardless of whether it was a community lot or their residential lot.  Before OFB a controllable sim could sleep on any community lot which had a bedroom setup.

I can only guess that maxis must have changed the code somehow so that option is no longer available for controlled sims, but other none controlled sims are still able to sleep on community lots.

Doc

I am not sure if this will help you much, but I use it so I don't have to keep track of those relationship numbers.  Its "AutoYak" by Pescadero (spelling might be wrong on his nick).  Here is the link to forum on his more awesome than you think site: http://www.moreawesomethanyou.com/smf/index.php?topic=207.msg4208#msg4208

Another thing you might try if you have Nightlife or later expansions, is to take them out on the town to downtown or another neighborhood area.  Either build or have a small motel/hotel installed into that area.  Then no matter how long they stay downtown, the college clock freezes and they can still do college assignments and/or term papers if a computer is also available at the hotel.

Doc