So far, I've been unable to reproduce this problem.  Here's what I've done so far…

• Start out with the default bookmarks in Safari and Camino.  This is a total of 57 bookmarks in 11 folders.  The idea is: enough to not be a trivial test, but not so much that it's going to take a long time to examine results.
• Create a Bookmarkshelf with Safari and Camino as Clients.
• After the initial Import, Export.
• Verify that Safari, Camino and Bookmarkshelf all have the same bookmarks.
• Click the Settings ▸ Simple Agents.
• Check the first 3 boxes on the left, to Import, Sort, and Export.
• Quit BookMacster (or don't quit BookMacster, I've tried it both ways, same result).
• In Camino, begin a long download which is going to take a couple hours.
• In Safari, click Show All Bookmarks.
• Drag a bookmark to a new location.
• Wait a few minutes for sync to occur.

Expected Result: Safari bookmarks should be sorted, but Camino should not, because the default Simple Agents do not attempt to export to a browser which cannot accept bookmarks while it is running, while it is running.  When I click in the menu BookMacster ▸ Logs, I should see an entry indicating Skipped write to running Camino.

Actual Result: As expected.

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However, in wildfox' description, a "message telling me to close the first browser" was mentioned.  This can happen if the Agent is set to Quit and relaunch browser if needed during the Export, and can be the case if Bookdog was set to do that, and Bookdog settings were imported.

So to test this, in the Bookmarkshelf window I clicked Settings ▸ Agents ▸ Advanced and changed the option on Export from Cancel if not allowed by browser running to Quit and relaunch browser if needed.  Then I repeated the test, with BookMacster running this time.  As expected, I got the message that Camino needed to be quit, and, of course, when I told Camino to quit, Camino told me that it had a download in progress.  Wildfox does not say how wildfox responded to this, but in my tests, I cancelled the quit, so that the download continued.  In that case I got the same result as originally; nothing happened to Camino bookmarks, as expected.

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I then ran into a snafu, unrelated to BookMacster, when updating to Mac OS 10.7.2.  So I'm going to delay further tests until tonight; maybe I'll do a screencast of what happens.  In the meantime, if wildfox or anyone else who has noticed such an issue wants to suggest a variation in my steps that will reproduce the problem, please do reply and tell us.

What the hell?
I would not be telling you this if empty bookmark folders was what I wanted!
These are empty because of BookMacster bug!
But I will tell you the unusual event that probably caused this, because it happened several times. 
FYI:
I had two browsers open. I was downloading a file in one.  In the other, I was rearranging bookmarks, and then closed the browser.  As it happened, the BM options were set to 'update when there are changes in bookmarks'.  So I get a message telling me to close the first browser, which I click to do, getting another message reminding me that I have a download in progress.

Prognosis:  In any event, BookMacster forces the user to work around it by requiring the user to close browsers so that it can do updates to the browsers.  This is sonotgoingtohappen.

Jerry,
Well, I had this thing whipped.  I finally had everything the way it needed to be.  Then, because I was looking at my Camino bookmarks, I saw that I had several EMPTY bookmark folders.  Same with the other clients.  I have blown it off and uninstalled, but I thought you should know.  Hellooooo Time Machine!  In case others have this problem, I am using latest version of SL with Intel Dual Core 2, 8G ram.

wildfox7 wrote on Oct 12^th, 2011 at 8:27pm:
I see that sentence.  You mean Dropbox.  Actually, that's not correct.  If you only have one Mac, you don't need Dropbox for BookMacster to work.

wildfox7 wrote on Oct 12^th, 2011 at 8:27pm:
Well, Dropbox is a nice app to have, but it really doesn't affect the automatic migration from Bookdog.  Let me know if you have any more trouble, and, if so, tell me what you want BookMacster to do.

The conflict between Bookdog and BookMacster is that they are both able to automatically maintain your browsers' (Safari, Firefox, Chrome, etc.) bookmarks.

• Bookdog does this via the action of Bookwatchdog feature.
• BookMacster does this via the action of its Agents feature.

If they're both trying to, for example, keep your Safari bookmarks sorted, this would be like having two cooks in the kitchen – they'll step on one another in ways that are difficult to imagine.

Bookwatchdog is an app which runs in the background.  To prevent these conflicts, upon launching, BookMacster checks to see if Bookwatchdog is running and if so quits it.  Because Bookdog could launch Bookwatchdog if you checked a preference in Bookdog, BookMacster quits Bookdog too.  The same thing happens when a BookMacster Agent launches to do its work.  This system has worked quite well; I've never seen any trouble reports indicating interference between Bookdog and BookMacster.

If you want to still use Bookdog, you may do so but you should click in the menu Bookdog ▸ Preferences.  Then click the Bookwatchdog tab and make sure that all the boxes are un-checked.

BookMacster does a lot of stuff but shouldn't be that hard for most users.  The automatic migration from Bookdog to BookMacster, I've recently realized, has some issues that cause confusion in some circumstances.  What do you want BookMacster to do?