This problem sounds like it may result from materials from the cytosol
streaming into the very small pipette tip.  One suggestion is to increase
the taper so that the pipette has a smaller length of extremely narrow bore.

Some other suggestions:

Use as pure water as you can find, 18.2 MOhm-cm,
reverse-osmosis/ion-exchange resin-filtered/and ultrafiltered.  Check the
pH of the dye and buffer it if necessary.  Finally, clean your pipette
glass before pulling by boiling in 6N HCl 3 times for 30 min each.  Then
boil in clean water for 4 to 5 times until the pH is stable.  You can
silanize the glass if simple cleanliness does not solve the problem, and
start with borosilicate glass.

Walter