As Paul says you haven't posted the complete code so we are all just guessing, but from what we have being given in you original code;
lcd.clear is called when "the down button has been pressed"
and
Value and parameter are changed when "Program_Mode and Value_Mode are HIGH"
Although it does look like it is in the if loop that calls lcd.clear (?). To get the best results from the forum, post the whole code (and use indenting) using the code button, i.e.
int Value;//value of parameter
int Value_change;//value of In- or Decrement
int setPin=0;//buttons connected to A0 pin of Arduino
int i;//to calculate how long the "select" button is pressed
int j;//to calculate how long no actions took place
int setPinValue;//value of analog input
boolean Program_Mode;
boolean Value_Mode;
//further code
void loop()
{
setPinValue = analogRead(setPin);
if ((setPinValue>=240)&&(setPinValue<420))//"Down" button pressed
{
lcd.clear();delay(20); j=0;
if ((Program_Mode==HIGH)&&(Value_Mode==HIGH))
{Value-=Value_change;}//decrement value of the paramerer chosen
else {parameter--;}//decrement parameter's number
}
//further code
}//end of void loop()