My OpenGL renderer works fine when I do simple forward rendering, but when I try to render to a frame buffer it does not display the last Vertex Array that I tell it to draw. I've changed the order in which they are passed and it always draws all but the last one.

I'm hoping that it's just something silly, like calling something out of order or forgetting to switch a value.

Here's the render code:

void OpenGLRenderer::render(std::vector<RenderObject>& scene, const Camera& camera)
{
	glBindFramebuffer(GL_FRAMEBUFFER, camera.targetBuffer); // remove to draw directly to back buffer
	glClear(GL_COLOR_BUFFER_BIT | GL_DEPTH_BUFFER_BIT);

	for (auto currentObject : scene)
	{
		glUseProgram(currentObject.shader);
		glBindVertexArray(currentObject.model);
		GLint currentModelSize;
		glGetBufferParameteriv(GL_ELEMENT_ARRAY_BUFFER, GL_BUFFER_SIZE, &currentModelSize);
		currentModelSize /= sizeof(GL_UNSIGNED_INT);
		GLuint transformLocation = glGetUniformLocation(currentObject.shader, "transform");
		glm::mat4 mvp = camera.projection * camera.view * currentObject.transform;
		glUniformMatrix4fv(transformLocation, 1, GL_FALSE, glm::value_ptr(mvp));
		glDrawElements(GL_TRIANGLES, currentModelSize, GL_UNSIGNED_INT, (void*)0);
	}
	glBindFramebuffer(GL_FRAMEBUFFER, 0);
}

and the main run loop:

while (isRunning)
{
	getInput();
	renderer.render(scene, camera);
	renderer.drawBufferToWindow(outputFrameBuffer.textureId, 800, 600); // remove to draw directly to backbuffer
	glfwSwapBuffers(window);	
}

the function do draw the framebuffer to the screen:

void OpenGLRenderer::drawBufferToWindow(const GLuint textureToRender, const unsigned int windowWidth, const unsigned int windowHeight)
{
	glBindFramebuffer(GL_FRAMEBUFFER, 0);	// set default (window) render target
	glClear(GL_COLOR_BUFFER_BIT | GL_DEPTH_BUFFER_BIT);
	glViewport(0, 0, windowWidth, windowHeight);
	glEnableVertexAttribArray(0); // make sure no other arrays are bound
	glBindBuffer(GL_ARRAY_BUFFER, windowRenderPoly);
	glVertexAttribPointer(0, 2, GL_FLOAT, GL_FALSE, 0, (void*)0);
	glBindTexture(GL_TEXTURE_2D, textureToRender);
	glUseProgram(windowRenderShader);
	glDrawArrays(GL_TRIANGLES, 0, 3);
	glDisableVertexAttribArray(0);
}

finally the renderObject class:

class RenderObject
{
public:
	unsigned int shader;
	unsigned int model;
	glm::mat4 transform;
};

I also found that if I remove the glClear command in the main render function it draws everything, even when drawing to the frame buffer. Obviously it can't actually be used this way though, as it leaves artifacts from previous frames.

Impossible to say what's wrong. A thing I don't understand: you define the buffer layout every frame, this is only done once usually. And it's good habit to store releavnt information like number of elements somewhere for direct use instead of asking opengl for the size and dividing by the number of elements.

And yes, when the clear is removed there is no clearing and the screen will fill up with all the drawing. I see two calls to glClear, maybe you clear away previously drawn things. After clearing once at the beginning of a frame one draws to the framebuffer observing good habits, and after that blit it to the default buffer for display.

One can clear the buffers to different colors to see if either drawing or blitting doesn't work.