Not without seeing code.

Things to check are, make sure you call release_bitmap whenever you call acquire_bitmap (and don't use any non-drawing routines between them), don't use rest() or the like to time your main loop (use timers), etc...

EDIT: What are the code tags on this board?
Here's how it was for testing:
[CODE]
...
LOCK_VARIABLE(logic_counter);
LOCK_FUNCTION(update_logic_counter);
install_int_ex(update_logic_counter, BPS_TO_TIMER(60));
...

void update_logic_counter()
{
++logic_counter;
} END_OF_FUNCTION(update_logic_counter)

void throttleFPS() {
if(Throttlefps ^ key[KEY_TILDE])
{
while(logic_counter < 1);
}
logic_counter = 0;
}
[/CODE]
Here's how it is normally:
[CODE]
void update_logic_counter()
{
++logic_counter;
} END_OF_FUNCTION(update_logic_counter)

void throttleFPS() {
if(Throttlefps ^ key[KEY_TILDE])
{
while(logic_counter < 1)
rest(1);
}
logic_counter = 0;
}
[/CODE]
As you can see, we do use rest() to control the timing, as I don't like pegging the CPU while I wait between frames; is this a bad idea?

Changing the timer to fire once per millisecond, and replacing the timing code with the following

void throttleFPS() {
  if(Throttlefps ^ key[KEY_TILDE])
  {
                al_trace("begin %d\n", logic_counter);
    while(logic_counter < 17);
                al_trace("end %d\n", logic_counter);
  }
  logic_counter = 0;
}

I get the following results:
Before waiting the counter's around 15-17, as I'm using triple buffering which apparently automatically vsyncs. After waiting the counter is usually 17, but occasionally 30-40.

Fair enough.

static long lastlow;
void throttleFPS() {
  LARGE_INTEGER freq;
  QueryPerformanceFrequency(&freq);
  LARGE_INTEGER currtime;
  QueryPerformanceCounter(&currtime);
  while(logic_counter < 1)
    rest(1);
  QueryPerformanceCounter(&currtime);
  long newtime = (currtime.LowPart*1000)/freq.LowPart;
  lastlow = newtime;
  logic_counter = 0;
}

The following is an excerpt of the output:

before: 7
after: 16
before: 8
after: 17
before: 7
after: 17
before: 6
after: 31
before: 3
after: 3
before: 5
after: 16
before: 5
after: 17
before: 4
after: 16
before: 4
after: 18
before: 3
after: 16
before: 3
after: 16
before: 2
after: 17
before: 2
after: 32
before: 1
after: 1
before: 2
after: 17
before: 2
after: 16
before: 2
after: 51
before: 2
after: 34
before: 20
after: 33
before: 2
after: 16
before: 2
after: 17
before: 1
after: 26

Overall what I'd expect, with some anomalies, as you can see, near the end, causing choppy game play.

That seems to have helped! Thank you.