Biolegato appears to incorrectly set ranges in menu sliders when the range includes numbers less than 0. For example, in $birch/dat/blprotein/menus/Alignment/tcoffee.item:

arg:GAPOPEN
argtype:slider
arglabel:Gap open penalty
argmin:-100
argmax:0
argvalue:-10

arg:GAPEXT
argtype:slider
arglabel:Gap extension penalty
argmin:-10
argmax:0
argvalue:-1


arg:COSPEN
argtype:slider
arglabel:Extension penalty for unalignable regions
argmin:-10
argmax:0
argvalue:-10

all three parameters are set, in the TCOFFEE menu, to have a range of 0..0. These numbers cannot be changed by typing in negative numbers. In blprotein, if you open Alignment --> TCOFFEE you'll see this.