Bugzilla

Bug 710056 (and dups of it, bug 717107, bug 720674, bug 723007) and bug 740740 are recently opened for loss of column selection/order change, and it sounds to happen frequently when auto-restart of Tb by software update.

Because column selection/column order is saved in .msf file like next, both are usually affected at same time, although only "loss of column order change" is observed, if "default column setting" is used and only column order only is changed, and if column selection data in .msf file is somehow lost or is not saved to .msf.
> @$${16{@
> <(BA
>     ={"threadCol":{"visible":false,"ordinal":"1"},"flaggedCol":{"visible":fals\
> e,"ordinal":"3"},"attachmentCol":{"visible":false,"ordinal":"5"},"subjectCol":\
> {"visible":true,"ordinal":"7"},"unreadButtonColHeader":{"visible":false,"ordin\
> al":"9"},"senderCol":{"visible":false,"ordinal":"11"},"recipientCol":{"visible\
> ":true,"ordinal":"21"},"junkStatusCol":{"visible":false,"ordinal":"13"},"recei\
> vedCol":{"visible":false,"ordinal":"35"},"dateCol":{"visible":true,"ordinal":"\
> 15"},"statusCol":{"visible":false,"ordinal":"17"},"sizeCol":{"visible":false,"\
> ordinal":"19"},"tagsCol":{"visible":true,"ordinal":"25"},"accountCol":{"visibl\
> e":true,"ordinal":"27"},"priorityCol":{"visible":false,"ordinal":"29"},"unread\
> Col":{"visible":false,"ordinal":"31"},"totalCol":{"visible":false,"ordinal":"3\
> 3"},"locationCol":{"visible":true,"ordinal":"37"},"idCol":{"visible":true,"ord\
> inal":"23"}})>[1:^9F(^B6^BA)]
> @$$}16}@

"Column selection/order chage of opened folder" is not written to .msf file immediately. If opened folder, it's written by folder close(MsgDB) and/or by MsgDB close upon termination of Tb. This is also true when "Appliy columns to..."(new from Tb 10?) is executed.
So, if Tb's termination is abnormal and column selection/order change is not written to .msf, the change is lost when Tb is restarted.

Is this kind of "abnormal termination of Tb" involved in your cases?