If your tick marks are being overridden, it might be that you're using Ticks rather than FrameTicks.
This is how I usually go about making my own tick marks. Unfortunately, that seems to happen a lot more often than I would like.
ticks[min_, max_, stepsz_, majorstep_, minorlength_, majorlength_,
labels_] :=
Table[{
i,
If[
labels \[And] Mod[Rationalize[i], Rationalize[majorstep]] == 0,
ToString[NumberForm[i, {Infinity, 1}]],
""
],
If[
Mod[Rationalize[i], Rationalize[majorstep]] == 0,
{majorlength, 0},
{minorlength, 0}
]
},
{i, min, max, stepsz}
]
Both Ticks and FrameTicks expect a list in the form { {x1, "x1", {innerlength, outerlength}}, {x2, "x2", {innerlength, outerlength}}, ...}, so my Table constructs a list with that format.
All of the arguments to the function should be numbers, except for labels which should be a boolean (True if you want tick labels on that axis, False otherwise).
One thing to watch out for is the NumberForm inside of ToString. I do that because otherwise MMA likes to output 1. instead of 1.0. So I'm currently forcing it to use 1 decimal place. The number of decimal places you want will probably vary from plot to plot. You could add it in as another argument to the function if you want.
Another tip that might be useful, is I have coded the outside tick length as zero, and my function only allows you to specify the inside length. If you want your ticks on the outside for some graph, you can change that.
This is how you would use the function:
ListLinePlot[
{},
Frame -> True,
FrameTicks -> {{
ticks[-1, 1, 0.1, 0.5, 0.01, 0.02, True],
ticks[-1, 1, 0.1, 0.5, 0.01, 0.02, False]},
{ticks[-1, 1, 0.1, 0.5, 0.01, 0.02, True],
ticks[-1, 1, 0.1, 0.5, 0.01, 0.02, False]}},
FrameStyle -> {{Black, Thickness[0.005]}, {Black,
Thickness[0.005]}, {Black, Thickness[0.005]}, {Black,
Thickness[0.005]}},
ImageSize -> 400,
ScalingFunctions -> {"Reverse", Identity}
]

FrameTicks -> {{left, right}, {bottom, top}}
I ended up using my custom ticks function for the left and right sides because Mathematica always shrinks my tick marks when I export (which is the reason I so often have to create my own ticks). This has the added benefit of making sure all the tick marks are the same length, but you could easily leave the left and right sides as Automatic if you like.