[Amps] trouble with TT centurion

[John]

Hello I am looking for some help I am new to using amplifiers in Ham radio I have been a ham for about 12 years but have just started using a amp.  I have a ten tec Jupiter and use two antennas   1)  a tenadyne LPA up at 65 feet tower is 150 feet away from the house.  this antenna is for 10,12,15,20, mtrs .  swr averages at 1.4 : 1     
2)  A Carolina Windom by w4cox  up about 40 feet and vertical portion about 50 feet away from the house with one of the legs of the dipole running over the houseabout 18 feet above the roof .  this antenna covers the remainder of the bands minus 160.  with out the amp both antennas work fine  however when I use the amp the LPA beam works fine but the Carolina Windom doesn't work well on 40 or 80 meters.  when used there I am told and I have listened  to the audio , I have a bad flutter to my audio once referred to as the sound of a machine gun .  Also when I tune the amp with low power on 40 or 80 I get a pulse sound that sounds like it comes from the amplifier .  The sound makes noise like sending cw dots from a keyer at about 15 words a minute when this happens the meters still look good where they are supposed to be .  I have all my station  grounded , I have checked all my jumper cables for shorts , ( although two patch cables are at about 6 feet too long ? )  when using the Carolina Windom I use a Nye Viking antenna tuner to get a flat match ( about 3:1 on 80 and 2:1 on 40 meters with out the tuner) my centurion is about 4 years old and I was instructed by TT to complete the mod needed to use with newer radios ie. jumper the diode etc.( mod completed )  by using the load and tune controls on the amp I can make these sounds go away but power put out by the amp goes down.  when I tune the amp for no crazy noise the audio is still fluttering .  and by the way my satellite tv on the upper floor is now bothered by TVI .  the phone is not affected.  The mic gain is at about 14percent and the speech proc is off on the Jupiter .   sorry for the long post .  any and all help will be appreciated .  John