Here is a list of every bug I've seen reported in 6.1 that I was able to confirm myself:

-/qme and /qmsg think they are /ame and /amsg
-/fopen creates a file even if -n isn't specified
-The colors dialog reverts the scheme after /color is used
-$decompress can crash mIRC and/or the entire PC
-$duration(N,3) screws up with large numbers
-/setlayer no longer can make mIRC transparent
-The right alt key no longer functions
-ctrl+break and ctrl+scrollock don't work correctly under WinXP
-$os returns .NET instead of 2003 for Windows Server 2003
-Paste confirm option incorrectly counts lines in a paste
-Dynamic menus (submenus) are completely broken
-"grayed text" was renamed "gray text" breaking all MTS themes
-Color codes > 16 are no longer parsed (N % 16) instead it just displays black
-Using the favorites dialog to join a channel you are already in makes the active window update, but not on the switchbar
-/hdec actually increases rather than decreases
-Multiline comments (/* */) don't work correctly if placed on a single line
-$fopen produces an error when given a file that is not opened
-Received files folder toolbar icon doesn't update if you change the received folder (for sounds) via alt+o, drop down menu will still say $mirddir\sounds
-Can no longer select multiple channels from the favorites dialog
-SOCKS proxies no longer seem to work (resolver problems)
-$fline with regex support always does a case insensitive comparison
-$base incorrectly rounds when converting using floating point
-$dllcall/$comcall crashes if given 3 parameters
-$comcall seems to always freeze even when the same operation using $com works fine
-/fwrite -n incorrectly reports the number of bytes written to the file
-Active "dot" on script editor toolbar button does not function as described
-/fopen -n deletes all text in an existing file
-Identifier warning feature incorrectly reports that $event does not exist when used in an alias that is called from an event
-Pressing the space bar to activate the nicklist menu causes the menu not to function
-$highlight(N).color returns the color +1
-Pressing f in a window that has no editbox no longer triggers the find dialog
-PNGs crash mIRC
-Topics are still truncated